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- Structure Factors (CIF)
- Structure Factors (CIF - gz)
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- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
2WYG|pdb_00002wyg
Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs
- PDB DOI: https://doi.org/10.2210/pdb2WYG/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2009-11-16 Released: 2010-12-01
- Deposition Author(s): Kleanthous, S.,Borthwick, A.D.,Brown, D.,Burns-Kurtis, C.L.,Campbell, M.,Chaudry, L.,Chan, C.,Clarte, M.,Convery, M.A.,Harling, J.D.,Hortense, E.,Irving, W.R.,Irvine, S.,Pateman, A.J.,Patikis, A.,Pinto, I.L.,Pollard, D.R.,Roethka, T.J.,Senger, S.,Shah, G.P.,Stelman, G.J.,Toomey, J.R.,Watson, N.S.,Whittaker, C.,Zhou, P.,Young, R.J.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 Å
- R-Value Free: 0.234 (Depositor)
- R-Value Work: 0.196 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.198 (Depositor)
Starting Model:experimental
View more details
This is version 1.5 of the entry. See complete history.
Literature
Download MendeleyStructure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Monoaryl P4 Motifs
Kleanthous, S., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chaudry, L., Chan, C., Clarte, M., Convery, M.A., Harling, J.D., Hortense, E., Irving, W.R., Irvine, S., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Roethka, T.J., Senger, S., Shah, G.P., Stelman, G.J., Toomey, J.R., Watson, N.S., Whittaker, C., Zhou, P., Young, R.J.(2010) Bioorg Med Chem Lett 20: 618
- PubMed: 20006499 Search on PubMed
- DOI: https://doi.org/10.1016/j.bmcl.2009.11.077
- Primary Citation of Related Structures:
2WYG,2WYJ - PubMed Abstract:
Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa inhibitors, incorporating neutral and basic monoaryl P4 groups, ultimately producing potent inhibitors with effective levels of anticoagulant activity and extended oral pharmacokinetic profiles. However, time dependant inhibition of Cytochrome P450 3A4 was a particular issue with this series.
Organizational Affiliation:
GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (461)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 44.23 kDa
- Atom Count: 2,439
- Modelled Residue Count: 280
- Deposited Residue Count: 388
- Unique protein chains: 2
Macromolecules
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 |
| FACTOR X 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 | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 461 Query on 461 Download Ideal Coordinates CCD File | C [auth A] | (E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1R)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE C20 H23 Cl F N3 O3 S2 AFDHTIFDRFSZDA-IUJLQVPDSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.88 Å
- R-Value Free: 0.234 (Depositor)
- R-Value Work: 0.196 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.198 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.673 | α = 90 |
| b = 72.814 | β = 90 |
| c = 78.509 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2010-12-01 Deposition Author(s): Kleanthous, S.,Borthwick, A.D.,Brown, D.,Burns-Kurtis, C.L.,Campbell, M.,Chaudry, L.,Chan, C.,Clarte, M.,Convery, M.A.,Harling, J.D.,Hortense, E.,Irving, W.R.,Irvine, S.,Pateman, A.J.,Patikis, A.,Pinto, I.L.,Pollard, D.R.,Roethka, T.J.,Senger, S.,Shah, G.P.,Stelman, G.J.,Toomey, J.R.,Watson, N.S.,Whittaker, C.,Zhou, P.,Young, R.J.
Revision History (Full details and data files)
- Version 1.0: 2010-12-01
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: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.5: 2024-11-13
Changes: 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.