Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.23 kDa 
• Atom Count: 2404 
• Residue Count: 285 
• Unique protein chains: 2

1F0S

Crystal Structure of Human Coagulation Factor XA Complexed with RPR208707

• DOI: 10.2210/pdb1F0S/pdb

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


• Deposited: 2000-05-17 Released: 2000-09-20 
• Deposition Author(s): Maignan, S., Guilloteau, J.P., Pouzieux, S., Choi-Sledeski, Y.M., Becker, M.R., Klein, S.I., Ewing, W.R., Pauls, H.W., Spada, A.P., Mikol, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Crystal structures of human factor Xa complexed with potent inhibitors.

Maignan, S., Guilloteau, J.P., Pouzieux, S., Choi-Sledeski, Y.M., Becker, M.R., Klein, S.I., Ewing, W.R., Pauls, H.W., Spada, A.P., Mikol, V.

(2000) J Med Chem 43: 3226-3232

• PubMed: 10966741 
• DOI: 10.1021/jm000940u
• Primary Citation of Related Structures:  
  1F0R, 1F0U, 1F0T, 1F0S, 1EZQ


• PubMed Abstract: 
  

Involved in the coagulation cascade, factor Xa (FXa) is a serine protease which has received great interest as a potential target for the development of new antithrombotics. Although there is a great wealth of structural data on thrombin complexes, few structures of ligand/FXa complexes have been reported, presumably because of the difficulty in growing crystals. Reproducible crystallization conditions for human des-Gla1-45 coagulation FXa have been found. This has led to an improvement in the diffraction quality of the crystals (about 2.1 A) when compared to the previously reported forms (2.3-2.8 A) thus providing a suitable platform for a structure-based drug design approach. A series of crystal structures of noncovalent inhibitors complexed with FXa have been determined, three of which are presented herein. These include compounds containing the benzamidine moiety and surrogates of the basic group. The benzamidine-containing compound binds in a canonical fashion typical of synthetic serine protease inhibitors. On the contrary, molecules that contain surrogates of the benzamidine group do not make direct hydrogen-bonding interactions with the carboxylate of Asp189 at the bottom of the S1 pocket. The structural data provide a likely explanation for the specificity of these inhibitors and a great aid in the design of bioavailable potent FXa inhibitors.

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Organizational Affiliation: 

Department of Structural Biology, Aventis Pharma, 13, Quai J. Guesde, F-94403 Vitry/Seine, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XA	A	254	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
COAGULATION FACTOR XA	B	134	Homo sapiens	Mutation(s): 0  Gene Names: F10 EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR2	A	THIENO[3,2-B]PYRIDINE-2-SULFONIC ACID [2-OXO-1-(1H-PYRROLO[2,3-C]PYRIDIN-2-YLMETHYL)-PYRROLIDIN-3-YL]-AMIDE C19 H17 N5 O3 S2 PLXOQMHGHDZMSX-AWEZNQCLSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PR2	Ki:  18   nM  BindingDB
PR2	Ki:  18   nM  Binding MOAD
PR2	Ki :  18   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.66	α = 90
b = 71.58	β = 90
c = 78.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-17 
• Released Date: 2000-09-20 
Deposition Author(s): Maignan, S., Guilloteau, J.P., Pouzieux, S., Choi-Sledeski, Y.M., Becker, M.R., Klein, S.I., Ewing, W.R., Pauls, H.W., Spada, A.P., Mikol, V.

Revision History 

• Version 1.0: 2000-09-20
  Type: Initial release
  
• Version 1.1: 2007-10-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance