2VH6|pdb_00002vh6
Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs
- PDB DOI: https://doi.org/10.2210/pdb2VH6/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2007-11-19 Released: 2008-12-16
- Deposition Author(s): Young, R.J.,Borthwick, A.D.,Brown, D.,Burns-Kurtis, C.L.,Campbell, M.,Chan, C.,Charbaut, M.,Chung, C.W.,Convery, M.A.,Kelly, H.A.,King, N.P.,Kleanthous, S.,Mason, A.M.,Pateman, A.J.,Patikis, A.N.,Pinto, I.L.,Pollard, D.R.,Senger, S.,Shah, G.P.,Toomey, J.R.,Watson, N.S.,Weston, H.E.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.242 (Depositor)
- R-Value Work: 0.197 (Depositor)
- R-Value Observed: 0.199 (Depositor)
wwPDB Validation 3D Report Full Report
Download MendeleyStructure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Biaryl P4 Motifs.
Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Chung, C.W., Convery, M.A., Kelly, H.A., Paul King, N., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A.N., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E.(2008) Bioorg Med Chem Lett 18: 23
- PubMed: 18054228 Search on PubMed
- DOI: https://doi.org/10.1016/j.bmcl.2007.11.023
- Primary Citation of Related Structures:
2VH6 - PubMed Abstract:
Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating biaryl P4 groups, producing highly potent inhibitors with encouraging oral pharmacokinetic profiles and significant but sub-optimal anticoagulant activities.
Organizational Affiliation:
GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. Rob.J.Young@gsk.com
Explore in 3D: Structure |Sequence Annotations |Validation Report |Ligand Interaction (GSV)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PQS (software)
Macromolecule Content
- Total Structure Weight: 44.32 kDa
- Atom Count: 2,433
- Modelled Residue Count: 286
- Deposited Residue Count: 388
- Unique protein chains: 2
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ACTIVATED FACTOR XA HEAVY CHAIN | 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 AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ACTIVATED FACTOR XA LIGHT CHAIN | 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 AnnotationsExpand | |||||
| |||||
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GSV Query on GSV Download Ideal Coordinates CCD File | C [auth A] | 2-(5-chlorothiophen-2-yl)-N-{(3S)-1-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-2-oxopyrrolidin-3-yl}ethanesulfonamide C23 H22 Cl F N2 O5 S3 MRKBPFVJGAHTFU-IBGZPJMESA-N |  | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.242 (Depositor)
- R-Value Work: 0.197 (Depositor)
- R-Value Observed: 0.199 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.959 | α = 90 |
| b = 72.309 | β = 90 |
| c = 78.976 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | phasing |
Deposition Data
- Released Date: 2008-12-16 Deposition Author(s): Young, R.J.,Borthwick, A.D.,Brown, D.,Burns-Kurtis, C.L.,Campbell, M.,Chan, C.,Charbaut, M.,Chung, C.W.,Convery, M.A.,Kelly, H.A.,King, N.P.,Kleanthous, S.,Mason, A.M.,Pateman, A.J.,Patikis, A.N.,Pinto, I.L.,Pollard, D.R.,Senger, S.,Shah, G.P.,Toomey, J.R.,Watson, N.S.,Weston, H.E.
Revision History (Full details and data files)
- Version 1.0: 2008-12-16
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: 2019-05-08
Changes: Data collection, Experimental preparation, Other - Version 1.4: 2024-10-23
Changes: Data collection, Database references, Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.