› 5tnt

X-ray diffraction
1.4Å resolution

Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors

Released:
DOI: 10.2210/pdb5tnt/pdb
PDB entry 5tnt coloured by chain, front view.
PDB entry 5tnt coloured by chain, side view.
PDB entry 5tnt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa inhibitors.
Sakurada I, Endo T, Hikita K, Hirabayashi T, Hosaka Y, Kato Y, Maeda Y, Matsumoto S, Mizuno T, Nagasue H, Nishimura T, Shimada S, Shinozaki M, Taguchi K, Takeuchi K, Yokoyama T, Hruza A, Reichert P, Zhang T, Wood HB, Nakao K, Furusako S
Bioorg Med Chem Lett 27 2622-2628 (2017)
PMID: 28408226

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: 26.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00740 (Residues: 227-461; Coverage: 54%)
Gene name: F9
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
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
Structure domains: Laminin

Ligands and Environments

3 bound ligands:
Ligand 7GQ 1 x 7GQ
Ligand NA 1 x NA
Ligand NHE 1 x NHE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: R3
Unit cell:
a: 99.084Å b: 99.084Å c: 94.68Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.147 0.146 0.161
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Discovery methods of coagulation-inhibiting drugs.
Gómez-Outes et al. (2017)
2 other articles

3 mentions without citation

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