Showing metabocard for Dabigatran (HMDB0250817)

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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:55:32 UTC

Update Date

2021-09-26 23:02:30 UTC

HMDB ID

HMDB0250817

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Dabigatran

Description

Dabigatran, also known as bibr 1048 or pradaxa, belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). Based on a literature review a significant number of articles have been published on Dabigatran. This compound has been identified in human blood as reported by (PMID:31557052). Dabigatran is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Dabigatran is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

MOL for HMDB0250817 (Dabigatran)

  Mrv1652309112109552D           35 38  0  0  0  0            999 V2000   -2.4685   -0.2146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -2.2136    0.5701    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    1.4289    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    4.2868    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.2136    1.9049    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.6985    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.5235    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.9360    0.5230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -4.7610    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.1735   -0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.9985   -0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -6.4110    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.9985    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.1735    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.2360    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.6485   -0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -7.6485    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0  1  2  1  0  0  0  0  2  3  1  0  0  0  0  3  4  2  0  0  0  0  4  5  1  0  0  0  0  5  6  2  0  0  0  0  6  7  1  0  0  0  0  7  8  2  0  0  0  0  3  8  1  0  0  0  0  6  9  1  0  0  0  0  9 10  2  0  0  0  0  9 11  1  0  0  0  0 11 12  1  0  0  0  0 12 13  1  0  0  0  0 13 14  1  0  0  0  0 14 15  2  0  0  0  0 14 16  1  0  0  0  0 11 17  1  0  0  0  0 17 18  2  0  0  0  0 18 19  1  0  0  0  0 19 20  2  0  0  0  0 20 21  1  0  0  0  0 21 22  2  0  0  0  0 17 22  1  0  0  0  0  4 23  1  0  0  0  0 23 24  2  0  0  0  0  2 24  1  0  0  0  0 24 25  1  0  0  0  0 25 26  1  0  0  0  0 26 27  1  0  0  0  0 27 28  2  0  0  0  0 28 29  1  0  0  0  0 29 30  2  0  0  0  0 30 31  1  0  0  0  0 31 32  2  0  0  0  0 27 32  1  0  0  0  0 30 33  1  0  0  0  0 33 34  2  0  0  0  0 33 35  1  0  0  0  0M  END

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3D MOL for HMDB0250817 (Dabigatran)

HMDB0250817     RDKit          3DDabigatran 60 63  0  0  0  0  0  0  0  0999 V2000    2.4638    3.0010   -0.2158 C   0  0  0  0  0  0  0  0  0  0  0  0    1.5105    1.9651    0.0429 N   0  0  0  0  0  0  0  0  0  0  0  0    1.8171    0.6944    0.3670 C   0  0  0  0  0  0  0  0  0  0  0  0    3.1862    0.1191    0.5190 C   0  0  0  0  0  0  0  0  0  0  0  0    3.6653   -0.4282   -0.7377 N   0  0  0  0  0  0  0  0  0  0  0  0    4.9580   -1.0171   -0.7594 C   0  0  0  0  0  0  0  0  0  0  0  0    5.7658   -1.0861    0.3584 C   0  0  0  0  0  0  0  0  0  0  0  0    7.0156   -1.6566    0.3340 C   0  0  0  0  0  0  0  0  0  0  0  0    7.5266   -2.1972   -0.8389 C   0  0  0  0  0  0  0  0  0  0  0  0    8.8625   -2.7922   -0.8091 C   0  0  0  0  0  0  0  0  0  0  0  0    9.4383   -3.3230   -1.8318 N   0  0  0  0  0  0  0  0  0  0  0  0    9.5628   -2.7805    0.4271 N   0  0  0  0  0  0  0  0  0  0  0  0    6.7414   -2.1398   -1.9617 C   0  0  0  0  0  0  0  0  0  0  0  0    5.4886   -1.5607   -1.9098 C   0  0  0  0  0  0  0  0  0  0  0  0    0.6439    0.0553    0.5240 N   0  0  0  0  0  0  0  0  0  0  0  0   -0.3803    0.8983    0.3052 C   0  0  0  0  0  0  0  0  0  0  0  0   -1.7841    0.7372    0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0   -2.6419    1.7565    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.0781    1.6830    0.1087 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.6937    2.7906   -0.2604 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.9684    0.6812    0.4498 N   0  0  0  0  0  0  0  0  0  0  0  0   -4.6663   -0.5955    0.9773 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.4500   -1.6843   -0.0556 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.1354   -2.9380    0.6601 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.9058   -4.0247    0.0752 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.0868   -2.9337    2.0402 O   0  0  0  0  0  0  0  0  0  0  0  0   -6.3865    0.9773    0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0   -6.9989    2.0241    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.3288    2.3218    0.7545 C   0  0  0  0  0  0  0  0  0  0  0  0   -9.0697    1.5304   -0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.4593    0.4952   -0.7441 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.1529    0.2332   -0.5622 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.0466    2.9919   -0.2339 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.6823    3.1698   -0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0    0.1695    2.1151   -0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0    1.9741    3.9661   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0    3.0967    2.7549   -1.0948 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1325    3.1792    0.6530 H   0  0  0  0  0  0  0  0  0  0  0  0    3.2199   -0.7013    1.2650 H   0  0  0  0  0  0  0  0  0  0  0  0    3.9004    0.8970    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1199   -0.4149   -1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0    5.3874   -0.6709    1.2831 H   0  0  0  0  0  0  0  0  0  0  0  0    7.5873   -1.6676    1.2681 H   0  0  0  0  0  0  0  0  0  0  0  0    8.9596   -3.3500   -2.7494 H   0  0  0  0  0  0  0  0  0  0  0  0    9.8374   -1.8685    0.8290 H   0  0  0  0  0  0  0  0  0  0  0  0    9.7938   -3.6476    0.9142 H   0  0  0  0  0  0  0  0  0  0  0  0    7.1254   -2.5545   -2.8745 H   0  0  0  0  0  0  0  0  0  0  0  0    4.8902   -1.5344   -2.8318 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.1050   -0.2524    0.5768 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.8761   -0.6366    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.5974   -0.8894    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.3452   -1.7950   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.6174   -1.4648   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0   -4.1264   -3.7711    2.6044 H   0  0  0  0  0  0  0  0  0  0  0  0   -6.4147    2.6406    1.5823 H   0  0  0  0  0  0  0  0  0  0  0  0   -8.8267    3.1297    1.2509 H   0  0  0  0  0  0  0  0  0  0  0  0  -10.1338    1.7305   -0.2584 H   0  0  0  0  0  0  0  0  0  0  0  0   -9.0168   -0.1323   -1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.6470    3.8526   -0.4549 H   0  0  0  0  0  0  0  0  0  0  0  0   -0.2184    4.1178   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0  1  2  1  0  2  3  1  0  3  4  1  0  4  5  1  0  5  6  1  0  6  7  2  0  7  8  1  0  8  9  2  0  9 10  1  0 10 11  2  3 10 12  1  0  9 13  1  0 13 14  2  0  3 15  2  0 15 16  1  0 16 17  2  0 17 18  1  0 18 19  1  0 19 20  2  0 19 21  1  0 21 22  1  0 22 23  1  0 23 24  1  0 24 25  2  0 24 26  1  0 21 27  1  0 27 28  2  0 28 29  1  0 29 30  2  0 30 31  1  0 31 32  2  0 18 33  2  0 33 34  1  0 34 35  2  0 35  2  1  0 14  6  1  0 35 16  1  0 32 27  1  0  1 36  1  0  1 37  1  0  1 38  1  0  4 39  1  0  4 40  1  0  5 41  1  0  7 42  1  0  8 43  1  0 11 44  1  0 12 45  1  0 12 46  1  0 13 47  1  0 14 48  1  0 17 49  1  0 22 50  1  0 22 51  1  0 23 52  1  0 23 53  1  0 26 54  1  0 28 55  1  0 29 56  1  0 30 57  1  0 31 58  1  0 33 59  1  0 34 60  1  0M  END

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3D SDF for HMDB0250817 (Dabigatran)

  Mrv1652309112109552D           35 38  0  0  0  0            999 V2000   -2.4685   -0.2146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -2.2136    0.5701    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.0000    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    1.4289    1.6500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    4.2868    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.2136    1.9049    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.6985    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.5235    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.9360    0.5230    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -4.7610    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.1735   -0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.9985   -0.1914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -6.4110    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.9985    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -5.1735    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.2360    0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.6485   -0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0   -7.6485    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0  1  2  1  0  0  0  0  2  3  1  0  0  0  0  3  4  2  0  0  0  0  4  5  1  0  0  0  0  5  6  2  0  0  0  0  6  7  1  0  0  0  0  7  8  2  0  0  0  0  3  8  1  0  0  0  0  6  9  1  0  0  0  0  9 10  2  0  0  0  0  9 11  1  0  0  0  0 11 12  1  0  0  0  0 12 13  1  0  0  0  0 13 14  1  0  0  0  0 14 15  2  0  0  0  0 14 16  1  0  0  0  0 11 17  1  0  0  0  0 17 18  2  0  0  0  0 18 19  1  0  0  0  0 19 20  2  0  0  0  0 20 21  1  0  0  0  0 21 22  2  0  0  0  0 17 22  1  0  0  0  0  4 23  1  0  0  0  0 23 24  2  0  0  0  0  2 24  1  0  0  0  0 24 25  1  0  0  0  0 25 26  1  0  0  0  0 26 27  1  0  0  0  0 27 28  2  0  0  0  0 28 29  1  0  0  0  0 29 30  2  0  0  0  0 30 31  1  0  0  0  0 31 32  2  0  0  0  0 27 32  1  0  0  0  0 30 33  1  0  0  0  0 33 34  2  0  0  0  0 33 35  1  0  0  0  0M  END> <DATABASE_ID>HMDB0250817> <DATABASE_NAME>hmdb> <SMILES>CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1> <INCHI_IDENTIFIER>InChI=1S/C25H25N7O3/c1-31-20-10-7-17(25(35)32(13-11-23(33)34)21-4-2-3-12-28-21)14-19(20)30-22(31)15-29-18-8-5-16(6-9-18)24(26)27/h2-10,12,14,29H,11,13,15H2,1H3,(H3,26,27)(H,33,34)> <INCHI_KEY>YBSJFWOBGCMAKL-UHFFFAOYSA-N> <FORMULA>C25H25N7O3> <MOLECULAR_WEIGHT>471.521> <EXACT_MASS>471.201887693> <JCHEM_ACCEPTOR_COUNT>8> <JCHEM_ATOM_COUNT>60> <JCHEM_AVERAGE_POLARIZABILITY>50.721727186883186> <JCHEM_BIOAVAILABILITY>1> <JCHEM_DONOR_COUNT>4> <JCHEM_FORMAL_CHARGE>0> <JCHEM_GHOSE_FILTER>0> <JCHEM_IUPAC>3-[1-(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-1,3-benzodiazol-5-yl)-N-(pyridin-2-yl)formamido]propanoic acid> <ALOGPS_LOGP>2.37> <JCHEM_LOGP>0.07681896906254265> <ALOGPS_LOGS>-3.68> <JCHEM_MDDR_LIKE_RULE>1> <JCHEM_NUMBER_OF_RINGS>4> <JCHEM_PHYSIOLOGICAL_CHARGE>0> <JCHEM_PKA>18.15826874847008> <JCHEM_PKA_STRONGEST_ACIDIC>3.3387181864924007> <JCHEM_PKA_STRONGEST_BASIC>12.521156598710041> <JCHEM_POLAR_SURFACE_AREA>150.21999999999997> <JCHEM_REFRACTIVITY>143.26109999999997> <JCHEM_ROTATABLE_BOND_COUNT>9> <JCHEM_RULE_OF_FIVE>1> <ALOGPS_SOLUBILITY>9.75e-02 g/l> <JCHEM_TRADITIONAL_IUPAC>dabigatran> <JCHEM_VEBER_RULE>0$$$$

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3D-SDF for HMDB0250817 (Dabigatran)

HMDB0250817     RDKit          3DDabigatran 60 63  0  0  0  0  0  0  0  0999 V2000    2.4638    3.0010   -0.2158 C   0  0  0  0  0  0  0  0  0  0  0  0    1.5105    1.9651    0.0429 N   0  0  0  0  0  0  0  0  0  0  0  0    1.8171    0.6944    0.3670 C   0  0  0  0  0  0  0  0  0  0  0  0    3.1862    0.1191    0.5190 C   0  0  0  0  0  0  0  0  0  0  0  0    3.6653   -0.4282   -0.7377 N   0  0  0  0  0  0  0  0  0  0  0  0    4.9580   -1.0171   -0.7594 C   0  0  0  0  0  0  0  0  0  0  0  0    5.7658   -1.0861    0.3584 C   0  0  0  0  0  0  0  0  0  0  0  0    7.0156   -1.6566    0.3340 C   0  0  0  0  0  0  0  0  0  0  0  0    7.5266   -2.1972   -0.8389 C   0  0  0  0  0  0  0  0  0  0  0  0    8.8625   -2.7922   -0.8091 C   0  0  0  0  0  0  0  0  0  0  0  0    9.4383   -3.3230   -1.8318 N   0  0  0  0  0  0  0  0  0  0  0  0    9.5628   -2.7805    0.4271 N   0  0  0  0  0  0  0  0  0  0  0  0    6.7414   -2.1398   -1.9617 C   0  0  0  0  0  0  0  0  0  0  0  0    5.4886   -1.5607   -1.9098 C   0  0  0  0  0  0  0  0  0  0  0  0    0.6439    0.0553    0.5240 N   0  0  0  0  0  0  0  0  0  0  0  0   -0.3803    0.8983    0.3052 C   0  0  0  0  0  0  0  0  0  0  0  0   -1.7841    0.7372    0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0   -2.6419    1.7565    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.0781    1.6830    0.1087 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.6937    2.7906   -0.2604 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.9684    0.6812    0.4498 N   0  0  0  0  0  0  0  0  0  0  0  0   -4.6663   -0.5955    0.9773 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.4500   -1.6843   -0.0556 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.1354   -2.9380    0.6601 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.9058   -4.0247    0.0752 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.0868   -2.9337    2.0402 O   0  0  0  0  0  0  0  0  0  0  0  0   -6.3865    0.9773    0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0   -6.9989    2.0241    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.3288    2.3218    0.7545 C   0  0  0  0  0  0  0  0  0  0  0  0   -9.0697    1.5304   -0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.4593    0.4952   -0.7441 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.1529    0.2332   -0.5622 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.0466    2.9919   -0.2339 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.6823    3.1698   -0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0    0.1695    2.1151   -0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0    1.9741    3.9661   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0    3.0967    2.7549   -1.0948 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1325    3.1792    0.6530 H   0  0  0  0  0  0  0  0  0  0  0  0    3.2199   -0.7013    1.2650 H   0  0  0  0  0  0  0  0  0  0  0  0    3.9004    0.8970    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1199   -0.4149   -1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0    5.3874   -0.6709    1.2831 H   0  0  0  0  0  0  0  0  0  0  0  0    7.5873   -1.6676    1.2681 H   0  0  0  0  0  0  0  0  0  0  0  0    8.9596   -3.3500   -2.7494 H   0  0  0  0  0  0  0  0  0  0  0  0    9.8374   -1.8685    0.8290 H   0  0  0  0  0  0  0  0  0  0  0  0    9.7938   -3.6476    0.9142 H   0  0  0  0  0  0  0  0  0  0  0  0    7.1254   -2.5545   -2.8745 H   0  0  0  0  0  0  0  0  0  0  0  0    4.8902   -1.5344   -2.8318 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.1050   -0.2524    0.5768 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.8761   -0.6366    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.5974   -0.8894    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.3452   -1.7950   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.6174   -1.4648   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0   -4.1264   -3.7711    2.6044 H   0  0  0  0  0  0  0  0  0  0  0  0   -6.4147    2.6406    1.5823 H   0  0  0  0  0  0  0  0  0  0  0  0   -8.8267    3.1297    1.2509 H   0  0  0  0  0  0  0  0  0  0  0  0  -10.1338    1.7305   -0.2584 H   0  0  0  0  0  0  0  0  0  0  0  0   -9.0168   -0.1323   -1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.6470    3.8526   -0.4549 H   0  0  0  0  0  0  0  0  0  0  0  0   -0.2184    4.1178   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0  1  2  1  0  2  3  1  0  3  4  1  0  4  5  1  0  5  6  1  0  6  7  2  0  7  8  1  0  8  9  2  0  9 10  1  0 10 11  2  3 10 12  1  0  9 13  1  0 13 14  2  0  3 15  2  0 15 16  1  0 16 17  2  0 17 18  1  0 18 19  1  0 19 20  2  0 19 21  1  0 21 22  1  0 22 23  1  0 23 24  1  0 24 25  2  0 24 26  1  0 21 27  1  0 27 28  2  0 28 29  1  0 29 30  2  0 30 31  1  0 31 32  2  0 18 33  2  0 33 34  1  0 34 35  2  0 35  2  1  0 14  6  1  0 35 16  1  0 32 27  1  0  1 36  1  0  1 37  1  0  1 38  1  0  4 39  1  0  4 40  1  0  5 41  1  0  7 42  1  0  8 43  1  0 11 44  1  0 12 45  1  0 12 46  1  0 13 47  1  0 14 48  1  0 17 49  1  0 22 50  1  0 22 51  1  0 23 52  1  0 23 53  1  0 26 54  1  0 28 55  1  0 29 56  1  0 30 57  1  0 31 58  1  0 33 59  1  0 34 60  1  0M  END

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PDB for HMDB0250817 (Dabigatran)

HEADER    PROTEIN                                 11-SEP-21   NONETITLE     NULL                                                        COMPND    NULL                                                        SOURCE    NULL                                                        KEYWDS    NULL                                                        EXPDTA    NULL                                                        AUTHOR    Marvin                                                      REVDAT   1   11-SEP-21         0                                  HETATM    1  C   UNK     0      -4.608  -0.401   0.000  0.00  0.00           C+0HETATM    2  N   UNK     0      -4.132   1.064   0.000  0.00  0.00           N+0HETATM    3  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0HETATM    4  C   UNK     0      -2.667   3.080   0.000  0.00  0.00           C+0HETATM    5  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0HETATM    6  C   UNK     0       0.000   3.080   0.000  0.00  0.00           C+0HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0HETATM    8  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0HETATM    9  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0HETATM   10  O   UNK     0       1.334   5.390   0.000  0.00  0.00           O+0HETATM   11  N   UNK     0       2.667   3.080   0.000  0.00  0.00           N+0HETATM   12  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0HETATM   13  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0HETATM   14  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0HETATM   15  O   UNK     0       8.002   3.080   0.000  0.00  0.00           O+0HETATM   16  O   UNK     0       6.668   5.390   0.000  0.00  0.00           O+0HETATM   17  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0HETATM   18  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0HETATM   19  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0HETATM   20  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0HETATM   21  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0HETATM   22  N   UNK     0       1.334   0.770   0.000  0.00  0.00           N+0HETATM   23  N   UNK     0      -4.132   3.556   0.000  0.00  0.00           N+0HETATM   24  C   UNK     0      -5.037   2.310   0.000  0.00  0.00           C+0HETATM   25  C   UNK     0      -6.577   2.310   0.000  0.00  0.00           C+0HETATM   26  N   UNK     0      -7.347   0.976   0.000  0.00  0.00           N+0HETATM   27  C   UNK     0      -8.887   0.976   0.000  0.00  0.00           C+0HETATM   28  C   UNK     0      -9.657  -0.357   0.000  0.00  0.00           C+0HETATM   29  C   UNK     0     -11.197  -0.357   0.000  0.00  0.00           C+0HETATM   30  C   UNK     0     -11.967   0.976   0.000  0.00  0.00           C+0HETATM   31  C   UNK     0     -11.197   2.310   0.000  0.00  0.00           C+0HETATM   32  C   UNK     0      -9.657   2.310   0.000  0.00  0.00           C+0HETATM   33  C   UNK     0     -13.507   0.976   0.000  0.00  0.00           C+0HETATM   34  N   UNK     0     -14.277  -0.357   0.000  0.00  0.00           N+0HETATM   35  N   UNK     0     -14.277   2.310   0.000  0.00  0.00           N+0CONECT    1    2                                                            CONECT    2    1    3   24                                                  CONECT    3    2    4    8                                                  CONECT    4    3    5   23                                                  CONECT    5    4    6                                                       CONECT    6    5    7    9                                                  CONECT    7    6    8                                                       CONECT    8    7    3                                                       CONECT    9    6   10   11                                                  CONECT   10    9                                                            CONECT   11    9   12   17                                                  CONECT   12   11   13                                                       CONECT   13   12   14                                                       CONECT   14   13   15   16                                                  CONECT   15   14                                                            CONECT   16   14                                                            CONECT   17   11   18   22                                                  CONECT   18   17   19                                                       CONECT   19   18   20                                                       CONECT   20   19   21                                                       CONECT   21   20   22                                                       CONECT   22   21   17                                                       CONECT   23    4   24                                                       CONECT   24   23    2   25                                                  CONECT   25   24   26                                                       CONECT   26   25   27                                                       CONECT   27   26   28   32                                                  CONECT   28   27   29                                                       CONECT   29   28   30                                                       CONECT   30   29   31   33                                                  CONECT   31   30   32                                                       CONECT   32   31   27                                                       CONECT   33   30   34   35                                                  CONECT   34   33                                                            CONECT   35   33                                                            MASTER        0    0    0    0    0    0    0    0   35    0   76    0END

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3D PDB for HMDB0250817 (Dabigatran)

COMPND    HMDB0250817HETATM    1  C1  UNL     1       2.464   3.001  -0.216  1.00  0.00           C  HETATM    2  N1  UNL     1       1.510   1.965   0.043  1.00  0.00           N  HETATM    3  C2  UNL     1       1.817   0.694   0.367  1.00  0.00           C  HETATM    4  C3  UNL     1       3.186   0.119   0.519  1.00  0.00           C  HETATM    5  N2  UNL     1       3.665  -0.428  -0.738  1.00  0.00           N  HETATM    6  C4  UNL     1       4.958  -1.017  -0.759  1.00  0.00           C  HETATM    7  C5  UNL     1       5.766  -1.086   0.358  1.00  0.00           C  HETATM    8  C6  UNL     1       7.016  -1.657   0.334  1.00  0.00           C  HETATM    9  C7  UNL     1       7.527  -2.197  -0.839  1.00  0.00           C  HETATM   10  C8  UNL     1       8.863  -2.792  -0.809  1.00  0.00           C  HETATM   11  N3  UNL     1       9.438  -3.323  -1.832  1.00  0.00           N  HETATM   12  N4  UNL     1       9.563  -2.780   0.427  1.00  0.00           N  HETATM   13  C9  UNL     1       6.741  -2.140  -1.962  1.00  0.00           C  HETATM   14  C10 UNL     1       5.489  -1.561  -1.910  1.00  0.00           C  HETATM   15  N5  UNL     1       0.644   0.055   0.524  1.00  0.00           N  HETATM   16  C11 UNL     1      -0.380   0.898   0.305  1.00  0.00           C  HETATM   17  C12 UNL     1      -1.784   0.737   0.340  1.00  0.00           C  HETATM   18  C13 UNL     1      -2.642   1.756   0.077  1.00  0.00           C  HETATM   19  C14 UNL     1      -4.078   1.683   0.109  1.00  0.00           C  HETATM   20  O1  UNL     1      -4.694   2.791  -0.260  1.00  0.00           O  HETATM   21  N6  UNL     1      -4.968   0.681   0.450  1.00  0.00           N  HETATM   22  C15 UNL     1      -4.666  -0.596   0.977  1.00  0.00           C  HETATM   23  C16 UNL     1      -4.450  -1.684  -0.056  1.00  0.00           C  HETATM   24  C17 UNL     1      -4.135  -2.938   0.660  1.00  0.00           C  HETATM   25  O2  UNL     1      -3.906  -4.025   0.075  1.00  0.00           O  HETATM   26  O3  UNL     1      -4.087  -2.934   2.040  1.00  0.00           O  HETATM   27  C18 UNL     1      -6.387   0.977   0.262  1.00  0.00           C  HETATM   28  C19 UNL     1      -6.999   2.024   0.915  1.00  0.00           C  HETATM   29  C20 UNL     1      -8.329   2.322   0.755  1.00  0.00           C  HETATM   30  C21 UNL     1      -9.070   1.530  -0.100  1.00  0.00           C  HETATM   31  C22 UNL     1      -8.459   0.495  -0.744  1.00  0.00           C  HETATM   32  N7  UNL     1      -7.153   0.233  -0.562  1.00  0.00           N  HETATM   33  C23 UNL     1      -2.047   2.992  -0.234  1.00  0.00           C  HETATM   34  C24 UNL     1      -0.682   3.170  -0.273  1.00  0.00           C  HETATM   35  C25 UNL     1       0.170   2.115  -0.001  1.00  0.00           C  HETATM   36  H1  UNL     1       1.974   3.966  -0.436  1.00  0.00           H  HETATM   37  H2  UNL     1       3.097   2.755  -1.095  1.00  0.00           H  HETATM   38  H3  UNL     1       3.132   3.179   0.653  1.00  0.00           H  HETATM   39  H4  UNL     1       3.220  -0.701   1.265  1.00  0.00           H  HETATM   40  H5  UNL     1       3.900   0.897   0.905  1.00  0.00           H  HETATM   41  H6  UNL     1       3.120  -0.415  -1.621  1.00  0.00           H  HETATM   42  H7  UNL     1       5.387  -0.671   1.283  1.00  0.00           H  HETATM   43  H8  UNL     1       7.587  -1.668   1.268  1.00  0.00           H  HETATM   44  H9  UNL     1       8.960  -3.350  -2.749  1.00  0.00           H  HETATM   45  H10 UNL     1       9.837  -1.868   0.829  1.00  0.00           H  HETATM   46  H11 UNL     1       9.794  -3.648   0.914  1.00  0.00           H  HETATM   47  H12 UNL     1       7.125  -2.554  -2.874  1.00  0.00           H  HETATM   48  H13 UNL     1       4.890  -1.534  -2.832  1.00  0.00           H  HETATM   49  H14 UNL     1      -2.105  -0.252   0.577  1.00  0.00           H  HETATM   50  H15 UNL     1      -3.876  -0.637   1.734  1.00  0.00           H  HETATM   51  H16 UNL     1      -5.597  -0.889   1.595  1.00  0.00           H  HETATM   52  H17 UNL     1      -5.345  -1.795  -0.714  1.00  0.00           H  HETATM   53  H18 UNL     1      -3.617  -1.465  -0.744  1.00  0.00           H  HETATM   54  H19 UNL     1      -4.126  -3.771   2.604  1.00  0.00           H  HETATM   55  H20 UNL     1      -6.415   2.641   1.582  1.00  0.00           H  HETATM   56  H21 UNL     1      -8.827   3.130   1.251  1.00  0.00           H  HETATM   57  H22 UNL     1     -10.134   1.730  -0.258  1.00  0.00           H  HETATM   58  H23 UNL     1      -9.017  -0.132  -1.412  1.00  0.00           H  HETATM   59  H24 UNL     1      -2.647   3.853  -0.455  1.00  0.00           H  HETATM   60  H25 UNL     1      -0.218   4.118  -0.512  1.00  0.00           H  CONECT    1    2   36   37   38CONECT    2    3   35CONECT    3    4   15   15CONECT    4    5   39   40CONECT    5    6   41CONECT    6    7    7   14CONECT    7    8   42CONECT    8    9    9   43CONECT    9   10   13CONECT   10   11   11   12CONECT   11   44CONECT   12   45   46CONECT   13   14   14   47CONECT   14   48CONECT   15   16CONECT   16   17   17   35CONECT   17   18   49CONECT   18   19   33   33CONECT   19   20   20   21CONECT   21   22   27CONECT   22   23   50   51CONECT   23   24   52   53CONECT   24   25   25   26CONECT   26   54CONECT   27   28   28   32CONECT   28   29   55CONECT   29   30   30   56CONECT   30   31   57CONECT   31   32   32   58CONECT   33   34   59CONECT   34   35   35   60END

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SMILES for HMDB0250817 (Dabigatran)

CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1

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INCHI for HMDB0250817 (Dabigatran)

InChI=1S/C25H25N7O3/c1-31-20-10-7-17(25(35)32(13-11-23(33)34)21-4-2-3-12-28-21)14-19(20)30-22(31)15-29-18-8-5-16(6-9-18)24(26)27/h2-10,12,14,29H,11,13,15H2,1H3,(H3,26,27)(H,33,34)

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Structure for HMDB0250817 (Dabigatran)

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3D Structure for HMDB0250817 (Dabigatran)

HMDB0250817     RDKit          3DDabigatran 60 63  0  0  0  0  0  0  0  0999 V2000    2.4638    3.0010   -0.2158 C   0  0  0  0  0  0  0  0  0  0  0  0    1.5105    1.9651    0.0429 N   0  0  0  0  0  0  0  0  0  0  0  0    1.8171    0.6944    0.3670 C   0  0  0  0  0  0  0  0  0  0  0  0    3.1862    0.1191    0.5190 C   0  0  0  0  0  0  0  0  0  0  0  0    3.6653   -0.4282   -0.7377 N   0  0  0  0  0  0  0  0  0  0  0  0    4.9580   -1.0171   -0.7594 C   0  0  0  0  0  0  0  0  0  0  0  0    5.7658   -1.0861    0.3584 C   0  0  0  0  0  0  0  0  0  0  0  0    7.0156   -1.6566    0.3340 C   0  0  0  0  0  0  0  0  0  0  0  0    7.5266   -2.1972   -0.8389 C   0  0  0  0  0  0  0  0  0  0  0  0    8.8625   -2.7922   -0.8091 C   0  0  0  0  0  0  0  0  0  0  0  0    9.4383   -3.3230   -1.8318 N   0  0  0  0  0  0  0  0  0  0  0  0    9.5628   -2.7805    0.4271 N   0  0  0  0  0  0  0  0  0  0  0  0    6.7414   -2.1398   -1.9617 C   0  0  0  0  0  0  0  0  0  0  0  0    5.4886   -1.5607   -1.9098 C   0  0  0  0  0  0  0  0  0  0  0  0    0.6439    0.0553    0.5240 N   0  0  0  0  0  0  0  0  0  0  0  0   -0.3803    0.8983    0.3052 C   0  0  0  0  0  0  0  0  0  0  0  0   -1.7841    0.7372    0.3397 C   0  0  0  0  0  0  0  0  0  0  0  0   -2.6419    1.7565    0.0774 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.0781    1.6830    0.1087 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.6937    2.7906   -0.2604 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.9684    0.6812    0.4498 N   0  0  0  0  0  0  0  0  0  0  0  0   -4.6663   -0.5955    0.9773 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.4500   -1.6843   -0.0556 C   0  0  0  0  0  0  0  0  0  0  0  0   -4.1354   -2.9380    0.6601 C   0  0  0  0  0  0  0  0  0  0  0  0   -3.9058   -4.0247    0.0752 O   0  0  0  0  0  0  0  0  0  0  0  0   -4.0868   -2.9337    2.0402 O   0  0  0  0  0  0  0  0  0  0  0  0   -6.3865    0.9773    0.2618 C   0  0  0  0  0  0  0  0  0  0  0  0   -6.9989    2.0241    0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.3288    2.3218    0.7545 C   0  0  0  0  0  0  0  0  0  0  0  0   -9.0697    1.5304   -0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0   -8.4593    0.4952   -0.7441 C   0  0  0  0  0  0  0  0  0  0  0  0   -7.1529    0.2332   -0.5622 N   0  0  0  0  0  0  0  0  0  0  0  0   -2.0466    2.9919   -0.2339 C   0  0  0  0  0  0  0  0  0  0  0  0   -0.6823    3.1698   -0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0    0.1695    2.1151   -0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0    1.9741    3.9661   -0.4363 H   0  0  0  0  0  0  0  0  0  0  0  0    3.0967    2.7549   -1.0948 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1325    3.1792    0.6530 H   0  0  0  0  0  0  0  0  0  0  0  0    3.2199   -0.7013    1.2650 H   0  0  0  0  0  0  0  0  0  0  0  0    3.9004    0.8970    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0    3.1199   -0.4149   -1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0    5.3874   -0.6709    1.2831 H   0  0  0  0  0  0  0  0  0  0  0  0    7.5873   -1.6676    1.2681 H   0  0  0  0  0  0  0  0  0  0  0  0    8.9596   -3.3500   -2.7494 H   0  0  0  0  0  0  0  0  0  0  0  0    9.8374   -1.8685    0.8290 H   0  0  0  0  0  0  0  0  0  0  0  0    9.7938   -3.6476    0.9142 H   0  0  0  0  0  0  0  0  0  0  0  0    7.1254   -2.5545   -2.8745 H   0  0  0  0  0  0  0  0  0  0  0  0    4.8902   -1.5344   -2.8318 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.1050   -0.2524    0.5768 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.8761   -0.6366    1.7340 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.5974   -0.8894    1.5952 H   0  0  0  0  0  0  0  0  0  0  0  0   -5.3452   -1.7950   -0.7137 H   0  0  0  0  0  0  0  0  0  0  0  0   -3.6174   -1.4648   -0.7444 H   0  0  0  0  0  0  0  0  0  0  0  0   -4.1264   -3.7711    2.6044 H   0  0  0  0  0  0  0  0  0  0  0  0   -6.4147    2.6406    1.5823 H   0  0  0  0  0  0  0  0  0  0  0  0   -8.8267    3.1297    1.2509 H   0  0  0  0  0  0  0  0  0  0  0  0  -10.1338    1.7305   -0.2584 H   0  0  0  0  0  0  0  0  0  0  0  0   -9.0168   -0.1323   -1.4125 H   0  0  0  0  0  0  0  0  0  0  0  0   -2.6470    3.8526   -0.4549 H   0  0  0  0  0  0  0  0  0  0  0  0   -0.2184    4.1178   -0.5119 H   0  0  0  0  0  0  0  0  0  0  0  0  1  2  1  0  2  3  1  0  3  4  1  0  4  5  1  0  5  6  1  0  6  7  2  0  7  8  1  0  8  9  2  0  9 10  1  0 10 11  2  3 10 12  1  0  9 13  1  0 13 14  2  0  3 15  2  0 15 16  1  0 16 17  2  0 17 18  1  0 18 19  1  0 19 20  2  0 19 21  1  0 21 22  1  0 22 23  1  0 23 24  1  0 24 25  2  0 24 26  1  0 21 27  1  0 27 28  2  0 28 29  1  0 29 30  2  0 30 31  1  0 31 32  2  0 18 33  2  0 33 34  1  0 34 35  2  0 35  2  1  0 14  6  1  0 35 16  1  0 32 27  1  0  1 36  1  0  1 37  1  0  1 38  1  0  4 39  1  0  4 40  1  0  5 41  1  0  7 42  1  0  8 43  1  0 11 44  1  0 12 45  1  0 12 46  1  0 13 47  1  0 14 48  1  0 17 49  1  0 22 50  1  0 22 51  1  0 23 52  1  0 23 53  1  0 26 54  1  0 28 55  1  0 29 56  1  0 30 57  1  0 31 58  1  0 33 59  1  0 34 60  1  0M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
BIBR 1048	HMDB
Etexilate mesylate, dabigatran	HMDB
Etexilate, dabigatran	HMDB
Mesylate, dabigatran etexilate	HMDB
N-((2-(((4-(Aminoiminomethyl)phenyl)amino)methyl)-1-methyl-1H-benzimidazol-5-yl)carbonyl)-N-2-pyridinyl-beta-alanine	HMDB
Pradaxa	HMDB
Dabigatran etexilate	HMDB
Dabigatran etexilate mesylate	HMDB

Chemical Formula

C₂₅H₂₅N₇O₃

Average Molecular Weight

471.521

Monoisotopic Molecular Weight

471.201887693

IUPAC Name

3-[1-(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-1,3-benzodiazol-5-yl)-N-(pyridin-2-yl)formamido]propanoic acid

Traditional Name

dabigatran

CAS Registry Number

Not Available

SMILES

CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1

InChI Identifier

InChI=1S/C25H25N7O3/c1-31-20-10-7-17(25(35)32(13-11-23(33)34)21-4-2-3-12-28-21)14-19(20)30-22(31)15-29-18-8-5-16(6-9-18)24(26)27/h2-10,12,14,29H,11,13,15H2,1H3,(H3,26,27)(H,33,34)

InChI Key

YBSJFWOBGCMAKL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds).

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzimidazoles

Sub Class

Not Available

Direct Parent

Benzimidazoles

Alternative Parents

Substituents

Benzimidazole
Aniline or substituted anilines
Phenylalkylamine
Secondary aliphatic/aromatic amine
Aralkylamine
Monocyclic benzene moiety
N-substituted imidazole
Pyridine
Benzenoid
Imidolactam
Heteroaromatic compound
Azole
Tertiary carboxylic acid amide
Imidazole
Amino acid
Amino acid or derivatives
Carboxamide group
Azacycle
Carboximidamide
Secondary amine
Amidine
Carboxylic acid amidine
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Amine
Organonitrogen compound
Carbonyl group
Organic nitrogen compound
Organooxygen compound
Organic oxide
Organic oxygen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

carboxamidine (CHEBI:70752)
beta-alanine derivative (CHEBI:70752)
pyridines (CHEBI:70752)
aromatic amide (CHEBI:70752)
benzimidazoles (CHEBI:70752)

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID:31557052)

Source

Exogenous

Exogenous (HMDB:HMDB0250817)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.37	ALOGPS
logP	0.077	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	3.34	ChemAxon
pKa (Strongest Basic)	12.52	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	150.22 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	143.26 m³·mol⁻¹	ChemAxon
Polarizability	50.72 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	203.361	30932474
DeepCCS	[M-H]-	200.965	30932474
DeepCCS	[M-2H]-	233.849	30932474
DeepCCS	[M+Na]+	209.274	30932474
AllCCS	[M+H]+	213.0	32859911
AllCCS	[M+H-H2O]+	211.1	32859911
AllCCS	[M+NH4]+	214.8	32859911
AllCCS	[M+Na]+	215.3	32859911
AllCCS	[M-H]-	205.0	32859911
AllCCS	[M+Na-2H]-	205.6	32859911
AllCCS	[M+HCOO]-	206.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dabigatran	CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1	5670.7	Standard polar	33892256
Dabigatran	CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1	4502.8	Standard non polar	33892256
Dabigatran	CN1C(CNC2=CC=C(C=C2)C(N)=N)=NC2=C1C=CC(=C2)C(=O)N(CCC(O)=O)C1=CC=CC=N1	5011.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Dabigatran,2TMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4756.4	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3987.2	Standard non polar	33892256
Dabigatran,2TMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	6233.6	Standard polar	33892256
Dabigatran,2TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4541.1	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3884.8	Standard non polar	33892256
Dabigatran,2TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	6268.6	Standard polar	33892256
Dabigatran,2TMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4640.8	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3956.4	Standard non polar	33892256
Dabigatran,2TMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	6564.6	Standard polar	33892256
Dabigatran,2TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4759.5	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4099.7	Standard non polar	33892256
Dabigatran,2TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6152.1	Standard polar	33892256
Dabigatran,2TMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4778.3	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4148.2	Standard non polar	33892256
Dabigatran,2TMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6303.1	Standard polar	33892256
Dabigatran,2TMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4816.3	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4149.4	Standard non polar	33892256
Dabigatran,2TMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6453.3	Standard polar	33892256
Dabigatran,2TMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4622.3	Semi standard non polar	33892256
Dabigatran,2TMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4095.9	Standard non polar	33892256
Dabigatran,2TMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6460.8	Standard polar	33892256
Dabigatran,3TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4588.5	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3924.9	Standard non polar	33892256
Dabigatran,3TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5729.6	Standard polar	33892256
Dabigatran,3TMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4636.6	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3971.8	Standard non polar	33892256
Dabigatran,3TMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5887.3	Standard polar	33892256
Dabigatran,3TMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4635.2	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3996.7	Standard non polar	33892256
Dabigatran,3TMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	6006.1	Standard polar	33892256
Dabigatran,3TMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4442.9	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3907.8	Standard non polar	33892256
Dabigatran,3TMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	6141.0	Standard polar	33892256
Dabigatran,3TMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4609.4	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4091.0	Standard non polar	33892256
Dabigatran,3TMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5806.3	Standard polar	33892256
Dabigatran,3TMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4635.1	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4110.5	Standard non polar	33892256
Dabigatran,3TMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5927.3	Standard polar	33892256
Dabigatran,3TMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4689.5	Semi standard non polar	33892256
Dabigatran,3TMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4159.4	Standard non polar	33892256
Dabigatran,3TMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5879.7	Standard polar	33892256
Dabigatran,4TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4490.8	Semi standard non polar	33892256
Dabigatran,4TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3907.6	Standard non polar	33892256
Dabigatran,4TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5482.4	Standard polar	33892256
Dabigatran,4TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4507.8	Semi standard non polar	33892256
Dabigatran,4TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3923.7	Standard non polar	33892256
Dabigatran,4TMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5571.6	Standard polar	33892256
Dabigatran,4TMS,isomer #3	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4566.1	Semi standard non polar	33892256
Dabigatran,4TMS,isomer #3	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3993.0	Standard non polar	33892256
Dabigatran,4TMS,isomer #3	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5536.0	Standard polar	33892256
Dabigatran,4TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4562.5	Semi standard non polar	33892256
Dabigatran,4TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4105.5	Standard non polar	33892256
Dabigatran,4TMS,isomer #4	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5457.1	Standard polar	33892256
Dabigatran,5TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	4460.4	Semi standard non polar	33892256
Dabigatran,5TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	3930.0	Standard non polar	33892256
Dabigatran,5TMS,isomer #1	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C)N([Si](C)(C)C)[Si](C)(C)C)C=C2)[Si](C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C)C3=CC=CC=N3)=CC=C21	5170.6	Standard polar	33892256
Dabigatran,2TBDMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5182.9	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4332.4	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #1	CN1C(CNC2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	6098.5	Standard polar	33892256
Dabigatran,2TBDMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4986.4	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4188.2	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #2	CN1C(CN(C2=CC=C(C(=N)N)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	6175.3	Standard polar	33892256
Dabigatran,2TBDMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5061.3	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4298.8	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #3	CN1C(CNC2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	6436.8	Standard polar	33892256
Dabigatran,2TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5172.5	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4387.7	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6037.7	Standard polar	33892256
Dabigatran,2TBDMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5155.5	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4480.5	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #5	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6143.4	Standard polar	33892256
Dabigatran,2TBDMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5236.5	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4458.6	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #6	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6218.3	Standard polar	33892256
Dabigatran,2TBDMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5018.7	Semi standard non polar	33892256
Dabigatran,2TBDMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4362.9	Standard non polar	33892256
Dabigatran,2TBDMS,isomer #7	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	6359.0	Standard polar	33892256
Dabigatran,3TBDMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5141.2	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4381.3	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #1	CN1C(CN(C2=CC=C(C(=N)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5716.5	Standard polar	33892256
Dabigatran,3TBDMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5147.7	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4466.6	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #2	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5843.4	Standard polar	33892256
Dabigatran,3TBDMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5199.4	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4469.4	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #3	CN1C(CNC2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5875.8	Standard polar	33892256
Dabigatran,3TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	5023.6	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	4340.4	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #4	CN1C(CN(C2=CC=C(C(N)=N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O[Si](C)(C)C(C)(C)C)C3=CC=CC=N3)=CC=C21	6104.7	Standard polar	33892256
Dabigatran,3TBDMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5116.8	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4512.8	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #5	CN1C(CN(C2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5781.2	Standard polar	33892256
Dabigatran,3TBDMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5181.0	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4509.6	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #6	CN1C(CN(C2=CC=C(C(=N)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)[Si](C)(C)C(C)(C)C)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5804.8	Standard polar	33892256
Dabigatran,3TBDMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5192.2	Semi standard non polar	33892256
Dabigatran,3TBDMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	4626.3	Standard non polar	33892256
Dabigatran,3TBDMS,isomer #7	CN1C(CNC2=CC=C(C(=N[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)C=C2)=NC2=CC(C(=O)N(CCC(=O)O)C3=CC=CC=N3)=CC=C21	5798.9	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4j-4637900000-58e7da523599fd7bb0a8	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dabigatran GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 10V, Positive-QTOF	splash10-00di-0001900000-bb51613c26fbcedb5b42	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 20V, Positive-QTOF	splash10-0c00-0013900000-f90f6c018330958a2fdb	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 40V, Positive-QTOF	splash10-0a5a-6937300000-912dc685f980b8885d43	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 10V, Negative-QTOF	splash10-0fl0-0009500000-058ffbf3cba49f32cec9	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 20V, Negative-QTOF	splash10-000t-0139100000-53fac2e2ba2dea2c1b8f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dabigatran 40V, Negative-QTOF	splash10-0fr5-2019000000-18e8bd8fd2ad810cc7ce	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

187412

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dabigatran

METLIN ID

Not Available

PubChem Compound

216210

PDB ID

Not Available

ChEBI ID

70752

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052]

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Showing metabocard for Dabigatran (HMDB0250817)

MOL for HMDB0250817 (Dabigatran)

3D MOL for HMDB0250817 (Dabigatran)

3D SDF for HMDB0250817 (Dabigatran)

3D-SDF for HMDB0250817 (Dabigatran)

PDB for HMDB0250817 (Dabigatran)

3D PDB for HMDB0250817 (Dabigatran)

SMILES for HMDB0250817 (Dabigatran)

INCHI for HMDB0250817 (Dabigatran)

Structure for HMDB0250817 (Dabigatran)

3D Structure for HMDB0250817 (Dabigatran)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra