› 1t4u

X-ray diffraction
2Å resolution

Crystal Structure Analysis of a novel Oxyguanidine bound to Thrombin

Released:
DOI: 10.2210/pdb1t4u/pdb
PDB entry 1t4u coloured by chain, front view.
PDB entry 1t4u coloured by chain, side view.
PDB entry 1t4u coloured by chain, top view.
Source organisms:
Primary publication:
Oxyguanidines. Part 2: Discovery of a novel orally active thrombin inhibitor through structure-based drug design and parallel synthesis.
Lu T, Markotan T, Coppo F, Tomczuk B, Crysler C, Eisennagel S, Spurlino J, Gremminger L, Soll RM, Giardino EC, Bone R
Bioorg Med Chem Lett 14 3727-31 (2004)
PMID: 15203151

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-133087 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Thrombin light chain Chain: L
Molecule details ›
Chain: L
Length: 26 amino acids
Theoretical weight: 3.08 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 334-359; Coverage: 4%)
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
Expression system: Not provided
UniProt:
  • Canonical: P00734 (Residues: 364-622; Coverage: 43%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Hirudin-2 Chain: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.49 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P28504 (Residues: 55-65; Coverage: 17%)

Ligands and Environments

1 bound ligand:
Ligand 81A 1 x 81A
1 modified residue:
Ligand TYS 1 x TYS

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR571
Spacegroup: C2
Unit cell:
a: 70.71Å b: 72.23Å c: 72.68Å
α: 90° β: 100.3° γ: 90°
R-values:
R R work R free
0.211 0.211 not available
Expression system: Not provided

Quick links

Citations

2 review citations

Natural guanidine derivatives.
Berlinck et al. (2005)
1 more

5 mentions without citation

Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data?
Ramírez et al. (2018)
4 more