› 2p3t

X-ray diffraction
1.92Å resolution

Crystal structure of human factor XA complexed with 3-Chloro-4-(2-methylamino-imidazol-1-ylmethyl)-thiophene-2-carboxylic acid [4-chloro-2-(5-chloro-pyridin-2-ylcarbamoyl)-6-methoxy-phenyl]-amide

Released:
DOI: 10.2210/pdb2p3t/pdb
PDB entry 2p3t coloured by chain, front view.
PDB entry 2p3t coloured by chain, side view.
PDB entry 2p3t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thiophene-anthranilamides as highly potent and orally available factor Xa inhibitors.
Ye B, Arnaiz DO, Chou YL, Griedel BD, Karanjawala R, Lee W, Morrissey MM, Sacchi KL, Sakata ST, Shaw KJ, Wu SC, Zhao Z, Adler M, Cheeseman S, Dole WP, Ewing J, Fitch R, Lentz D, Liang A, Light D, Morser J, Post J, Rumennik G, Subramanyam B, Sullivan ME, Vergona R, Walters J, Wang YX, White KA, Whitlow M, Kochanny MJ
J Med Chem 50 2967-80 (2007)
PMID: 17536795

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Thr and then Arg-|-Ile bonds in prothrombin to form thrombin.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133209 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Factor X light chain Chain: A
Molecule details ›
Chain: A
Length: 52 amino acids
Theoretical weight: 5.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00742 (Residues: 127-178; Coverage: 11%)
Gene name: F10
Sequence domains: Coagulation Factor Xa inhibitory site
Structure domains: Laminin
Activated factor Xa heavy chain Chain: B
Molecule details ›
Chain: B
Length: 233 amino acids
Theoretical weight: 26.35 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00742 (Residues: 235-467; Coverage: 51%)
Gene name: F10
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

3 bound ligands:
Ligand CA 1 x CA
Ligand CL 1 x CL
Ligand 993 1 x 993
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P212121
Unit cell:
a: 57.06Å b: 72.51Å c: 78.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.219

Quick links

Citations

4 review citations

Oral, direct thrombin and factor Xa inhibitors: the replacement for warfarin, leeches, and pig intestines?
Straub et al. (2011)
3 more

1 mention without citation

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.
Smith et al. (2011)