› 3m36

X-ray diffraction
2.15Å resolution

Factor XA in complex with the inhibitor 1-[3-(aminomethyl)phenyl]-N-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC423)

Released:
DOI: 10.2210/pdb3m36/pdb
PDB entry 3m36 coloured by chain, front view.
PDB entry 3m36 coloured by chain, side view.
PDB entry 3m36 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of 1-(2-aminomethylphenyl)-3-trifluoromethyl-N- [3-fluoro-2'-(aminosulfonyl)[1,1'-biphenyl)]-4-yl]-1H-pyrazole-5-carboxyamide (DPC602), a potent, selective, and orally bioavailable factor Xa inhibitor(1).
Pruitt JR, Pinto DJ, Galemmo RA, Alexander RS, Rossi KA, Wells BL, Drummond S, Bostrom LL, Burdick D, Bruckner R, Chen H, Smallwood A, Wong PC, Wright MR, Bai S, Luettgen JM, Knabb RM, Lam PY, Wexler RR
J Med Chem 46 5298-315 (2003)
PMID: 14640539

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 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):
Activated factor Xa heavy chain Chain: A
Molecule details ›
Chain: A
Length: 234 amino acids
Theoretical weight: 26.45 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00742 (Residues: 235-468; Coverage: 51%)
Gene name: F10
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Factor X light chain Chain: L
Molecule details ›
Chain: L
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

Ligands and Environments

2 bound ligands:
Ligand M35 1 x M35
Ligand CA 1 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 5ID-B
Spacegroup: P212121
Unit cell:
a: 56.8Å b: 72.3Å c: 77.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.264

Quick links

Citations

4 review citations

Strategies to improve oral drug bioavailability.
Gomez-Orellana I. (2005)
3 more

1 mention without citation

A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa.
Kundu et al. (2021)