2P3U | pdb_00002p3u

Crystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663}

• PDB DOI: https://doi.org/10.2210/pdb2P3U/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-03-09 Released: 2007-09-11 
• Deposition Author(s): Adler, M., Whitlow, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human factor XA complexed with 3-chloro-N-(4-chloro-2-{[(5-chloropyridin-2-yl)amino]carbonyl}-6-methoxyphenyl)-4-[(1-methyl-1H-imidazol-2-yl)methyl]thiophene-2-carboxamide {Pfizer 320663}

Adler, M.

Not Published 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2,524 
• Modeled Residue Count: 284 
• Deposited Residue Count: 285 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	233	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
663	E [auth B]	3-CHLORO-N-(4-CHLORO-2-{[(5-CHLOROPYRIDIN-2-YL)AMINO]CARBONYL}-6-METHOXYPHENYL)-4-[(1-METHYL-1H-IMIDAZOL-2-YL)METHYL]THIOPHENE-2-CARBOXAMIDE C23 H18 Cl3 N5 O3 S WBFPCLIRIGEEBD-UHFFFAOYSA-N
CA	C [auth B], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.014	α = 90
b = 71.717	β = 90
c = 78.651	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Adler, M., Whitlow, M.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2026-03-11
  Changes: Database references, Structure summary