	235,183 Structures from the PDB
	1,068,577 Computed Structure Models (CSM)

2Y80|pdb_00002y80

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs

PDB DOI: https://doi.org/10.2210/pdb2Y80/pdb

Deposited: 2011-02-02 Released: 2011-03-16
Deposition Author(s): Young, R.J.,Adams, C.,Blows, M.,Brown, D.,Burns-Kurtis, C.L.,Chaudry, L.,Chan, C.,Convery, M.A.,Davies, D.E.,Exall, A.M.,Foster, G.,Harling, J.D.,Hortense, E.,Irving, W.R.,Irvine, S.,Jackson, S.,Kleanthous, S.,Pateman, A.J.,Patikis, A.N.,Roethka, T.J.,Senger, S.,Stelman, G.J.,Toomey, J.R.,West, R.I.,Whittaker, C.,Zhou, P.,Watson, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.241 (Depositor)
R-Value Work:
0.189 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs.

Young, R.J., Adams, C., Blows, M., Brown, D., Burns-Kurtis, C.L., Chan, C., Chaudry, L., Convery, M.A., Davies, D.E., Exall, A.M., Foster, G., Harling, J.D., Hortense, E., Irvine, S., Irving, W.R., Jackson, S., Kleanthous, S., Pateman, A.J., Patikis, A.N., Roethka, T.J., Senger, S., Stelman, G.J., Toomey, J.R., West, R.I., Whittaker, C., Zhou, P., Watson, N.S.

(2011) Bioorg Med Chem Lett 21: 1582

PubMed: 21349710 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.01.131
Primary Citation of Related Structures:
2Y7Z,2Y80,2Y81,2Y82

PubMed Abstract:
The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans.

Organizational Affiliation

GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, United Kingdom. Rob.J.Young@gsk.com

Macromolecule Content

Total Structure Weight: 44.31 kDa
Atom Count: 2,507
Modelled Residue Count: 288
Deposited Residue Count: 388
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	A	254	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	B	134	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
PHAROS: P00742 GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
439 Query on 439 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	6-CHLORO-N-{(3S)-1-[(1S)-1-(DIMETHYLAMINO)-2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE C₂₅ H₂₆ Cl N₃ O₃ S DBFTVRMJVISJEX-BJKOFHAPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
439	BindingDB: 2Y80	Ki: min: 3, max: 9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.241 (Depositor)
R-Value Work: 0.189 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.727	α = 90
b = 72.012	β = 90
c = 78.689	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-16
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-10-16
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary