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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.294 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Structure-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 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.092
• Primary Citation 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.

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Organizational Affiliation: 
• Bristol-Myers Squibb Research and Development, PO Box 5400, Princeton, NJ 08543, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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	A	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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FXA	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

Binding Affinity Annotations
ID	Source	Binding Affinity
FXA	BindingDB:  3CEN	Ki: 5.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.294 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.249 (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 Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-20 
Deposition Author(s): Chang, C.-H.

Revision History  

• 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