- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
3CEN|pdb_00003cen
Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl) amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide
- PDB DOI: https://doi.org/10.2210/pdb3CEN/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2008-02-29 Released: 2008-05-20
- Deposition Author(s): Chang, C.-H.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.294 (Depositor), 0.290 (DCC)
- R-Value Work: 0.249 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.251 (Depositor)
This is version 1.2 of the entry. See complete history.
Literature
Download MendeleyStructure-Activity Relationships of Anthranilamide-Based Factor Xa Inhibitors Containing Piperidinone and Pyridinone P4 Moieties
Corte, J.R., Fang, T., Pinto, D.J.P., Han, W., Hu, Z., Jiang, X.-J., Li, Y.-L., Gauuan, J.F., Hadden, M., Orton, D., Rendina, A.R., Luettgen, J.M., Wong, P.C., He, K., Morin, P., Chang, C.-H., Cheney, D.L., Knabb, R.M., Wexler, R.R., Lam, P.Y.S.(2008) Bioorg Med Chem Lett 18: 2845-2849
- PubMed: 18424044 Search on PubMed
- DOI: https://doi.org/10.1016/j.bmcl.2008.03.092
- Primary Citation of Related Structures:
3CEN - PubMed Abstract:
Introduction of the phenyl piperidinone and phenyl pyridinone P4 moieties in the anthranilamide scaffold led to potent, selective, and orally bioavailable inhibitors of factor Xa. Anthranilamide 28 displayed comparable efficacy to apixaban in the rabbit arteriovenous-shunt (AV) thrombosis model.
- Bristol-Myers Squibb Research and Development, PO Box 5400, Princeton, NJ 08543, USA. james.corte@bms.com
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (FXA)
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: 32.52 kDa
- Atom Count: 2,550
- Modeled Residue Count: 286
- Deposited Residue Count: 286
- Unique protein chains: 2
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| COAGULATION FACTOR X, HEAVY CHAIN | 234 | 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 |
| COAGULATION FACTOR X, LIGHT CHAIN | B [auth L] | 52 | 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 | |
| FXA Query on FXA Download Ideal Coordinates CCD File | C [auth A] | N-(2-(((5-CHLORO-2-PYRIDINYL)AMINO)SULFONYL)PHENYL)-4-(2-OXO-1(2H)-PYRIDINYL)BENZAMIDE C23 H17 Cl N4 O4 S MIJGLXFQYBTIFY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.294 (Depositor), 0.290 (DCC)
- R-Value Work: 0.249 (Depositor), 0.240 (DCC)
- R-Value Observed: 0.251 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.9 | α = 90 |
| b = 72.5 | β = 90 |
| c = 78.8 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| CNX | refinement |
Entry History
Deposition Data
- Released Date: 2008-05-20 Deposition Author(s): Chang, C.-H.
Revision History (Full details and data files)
- Version 1.0: 2008-05-20
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, 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.