› 6x5j

X-ray diffraction
2.51Å resolution

Discovery of Hydroxy Pyrimidine Factor IXa Inhibitors

Released:
DOI: 10.2210/pdb6x5j/pdb
PDB entry 6x5j coloured by chain, front view.
PDB entry 6x5j coloured by chain, side view.
PDB entry 6x5j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of hydroxy pyrimidine Factor IXa inhibitors.
Jayne CL, Andreani T, Chan TY, Chelliah MV, Clasby MC, Dwyer M, Eagen KA, Fried S, Greenlee WJ, Guo Z, Hawes B, Hruza A, Ingram R, Keertikar KM, Neelamkavil S, Reichert P, Xia Y, Chackalamannil S
Bioorg Med Chem Lett 30 127279 (2020)
PMID: 32527459

Function and Biology Details

Reaction catalysed: 
Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa.
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-133191 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Coagulation factor IXa heavy chain Chain: A
Molecule details ›
Chain: A
Length: 235 amino acids
Theoretical weight: 26.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Sequence domains: Trypsin
Coagulation factor IXa light chain Chain: B
Molecule details ›
Chain: B
Length: 62 amino acids
Theoretical weight: 6.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 130-191; Coverage: 14%)
Gene name: F9
Sequence domains: Coagulation Factor Xa inhibitory site

Ligands and Environments

4 bound ligands:
Ligand GOL 2 x GOL
Ligand 6NH 1 x 6NH
Ligand NA 1 x NA
Ligand CIT 4 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P43212
Unit cell:
a: 100.548Å b: 100.548Å c: 98.495Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.225
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

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