3CEN

Factor XA in complex with the inhibitor N-(2-(((5-chloro-2-pyridinyl) amino)sulfonyl)phenyl)-4-(2-oxo-1(2H)-pyridinyl)benzamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Bristol-Myers Squibb Research and Development, PO Box 5400, Princeton, NJ 08543, USA. james.corte@bms.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COAGULATION FACTOR X, HEAVY CHAIN234Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COAGULATION FACTOR X, LIGHT CHAINB [auth L]52Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D 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
Binding Affinity Annotations 
IDSourceBinding Affinity
FXA PDBBind:  3CEN Ki: 5.5 (nM) from 1 assay(s)
BindingDB:  3CEN Ki: 5.5 (nM) from 1 assay(s)
Binding MOAD:  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 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.9α = 90
b = 72.5β = 90
c = 78.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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