PDBe 4loy

X-ray diffraction
1.77Å resolution

Crystal Structure Analysis of thrombin in complex with compound D57, 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2- oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1- yl)-3-oxopropyl]amide (SAR107375)

Released:

Function and Biology Details

Reaction catalysed:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 257 amino acids
Theoretical weight: 29.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-620; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-2 Chain: I
Molecule details ›
Chain: I
Length: 10 amino acids
Theoretical weight: 1.36 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P09945 (Residues: 62-71; Coverage: 15%)
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 27 amino acids
Theoretical weight: 3.19 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 334-360; Coverage: 5%)
Gene name: F2

Ligands and Environments

3 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: C2
Unit cell:
a: 70.522Å b: 71.196Å c: 73.14Å
α: 90° β: 100.91° γ: 90°
R-values:
R R work R free
0.178 0.177 0.208
Expression system: Not provided