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X-ray diffraction
2.25Å resolution

Discovery and Clinical Evaluation of RWJ-671818, a Thrombin Inhibitor with an Oxyguanidine P1 Motif

Released:
DOI: 10.2210/pdb3ldx/pdb
PDB entry 3ldx coloured by chain, front view.
PDB entry 3ldx coloured by chain, side view.
PDB entry 3ldx coloured by chain, top view.
Source organisms:
Entry author: Spurlino JC

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
Expression system: Not provided
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
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 variant-1 Chain: I
Molecule details ›
Chain: I
Length: 11 amino acids
Theoretical weight: 1.41 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
UniProt:
  • Canonical: P01050 (Residues: 55-65; Coverage: 17%)

Ligands and Environments

1 bound ligand:
Ligand NLI 1 x NLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 71.099Å b: 72.008Å c: 73.412Å
α: 90° β: 101.06° γ: 90°
R-values:
R R work R free
0.18 0.175 0.224
Expression system: Not provided

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