› 3tu7

X-ray diffraction
2.49Å resolution

Human alpha-thrombin complexed with N-(methylsulfonyl)-D-phenylalanyl-N-((1-carbamimidoyl-4-piperidinyl)methyl)-l-prolinamide (BMS-189664)

Released:
DOI: 10.2210/pdb3tu7/pdb
PDB entry 3tu7 coloured by chain, front view.
PDB entry 3tu7 coloured by chain, side view.
PDB entry 3tu7 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular design and structure--activity relationships leading to the potent, selective, and orally active thrombin active site inhibitor BMS-189664.
Das J, Kimball SD, Hall SE, Han WC, Iwanowicz E, Lin J, Moquin RV, Reid JA, Sack JS, Malley MF, Chang CY, Chong S, Wang-Iverson DB, Roberts DG, Seiler SM, Schumacher WA, Ogletree ML
Bioorg Med Chem Lett 12 45-9 (2002)
PMID: 11738570

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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133065 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 36 amino acids
Theoretical weight: 4.1 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 328-363; Coverage: 6%)
Gene name: F2
Sequence domains: Thrombin light chain
Thrombin heavy chain Chain: H
Molecule details ›
Chain: H
Length: 259 amino acids
Theoretical weight: 29.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin variant-1 Chain: I
Molecule details ›
Chain: I
Length: 12 amino acids
Theoretical weight: 1.55 KDa
Source organism: Hirudo medicinalis
UniProt:
  • Canonical: P01050 (Residues: 54-65; Coverage: 19%)

Ligands and Environments

1 bound ligand:
Ligand 0BM 1 x 0BM
1 modified residue:
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 164.219Å b: 48.952Å c: 43.631Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.159 0.23

Quick links

Citations

1 review citation

Progress in the design of low molecular weight thrombin inhibitors.
Srivastava et al. (2005)
8 other articles

1 mention without citation

Integrating pharmacokinetics and network analysis to investigate the mechanism of Moutan Cortex in blood-heat and blood stasis syndrome.
Ye et al. (2022)