1KSN

Crystal Structure of Human Coagulation Factor XA Complexed with FXV673

• PDB DOI: https://doi.org/10.2210/pdb1KSN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2002-01-14 Released: 2002-06-19 
• Deposition Author(s): Maignan, S., Guilloteau, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Optimization of the beta-aminoester class of factor Xa inhibitors. Part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity.

Guertin, K.R., Gardner, C.J., Klein, S.I., Zulli, A.L., Czekaj, M., Gong, Y., Spada, A.P., Cheney, D.L., Maignan, S., Guilloteau, J.P., Brown, K.D., Colussi, D.J., Chu, V., Heran, C.L., Morgan, S.R., Bentley, R.G., Dunwiddie, C.T., Leadley, R.J., Pauls, H.W.

(2002) Bioorg Med Chem Lett 12: 1671-1674

• PubMed: 12039587 
• DOI: https://doi.org/10.1016/s0960-894x(02)00213-5
• Primary Citation of Related Structures:  
  1KSN


• PubMed Abstract: 
  

  Further optimization of the beta-aminoester class of factor Xa (fXa) inhibitors is described culminating in the identification of 9c (FXV673), a potent and selective factor Xa inhibitor with excellent in vivo anticoagulant activity. An X-ray structure of FXV673 bound to human fXa is also presented. Based on its selectivity, potent in vivo activity and favorable pre-clinical safety profile, FXV673 was selected for further development and is currently undergoing clinical trials.

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Organizational Affiliation: 

Drug Innovation and Approval, Aventis Pharmaceuticals, Route 202-206, Bridgewater, NJ 08807, 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: 44.25 kDa 
• Atom Count: 2,405 
• Modelled Residue Count: 286 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XA	A	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XA	B	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FXV	D [auth A]	METHYL-3-(4'-N-OXOPYRIDYLPHENOYL)-3-METHYL-2-(M-AMIDINOBENZYL)-PROPIONATE C25 H27 N4 O4 PFGVNLZDWRZPJW-OPAMFIHVSA-O
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FXV	Binding MOAD:  1KSN	Ki: 0.4 (nM) from 1 assay(s)
	PDBBind:  1KSN	Ki: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.81	α = 90
b = 71.6	β = 90
c = 79.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-06-19 
Deposition Author(s): Maignan, S., Guilloteau, J.P.

Revision History  

• Version 1.0: 2002-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance