3C1K image
Deposition Date 2008-01-23
Release Date 2008-03-18
Last Version Date 2024-11-20
Entry Detail
PDB ID:
3C1K
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
Crystal structure of thrombin in complex with inhibitor 15
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Hirudo medicinalis (Taxon ID: 6421)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.84 Å
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 1 2 1
3C1K validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Prothrombin
Gene (Uniprot):F2
Chain IDs:A
Chain Length:287
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P00734 Pfam ID:PF09396, PF00089 EC:3.4.21.5
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hirugen
Chain IDs:B
Chain Length:11
Number of Molecules:1
Biological Source:Hirudo medicinalis
UniProt ID:P28511
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TYS B TYR O-SULFO-L-TYROSINE
Ligand Molecules
T15
Primary Citation
Structure-based design of novel groups for use in the P1 position of thrombin inhibitor scaffolds. Part 2: N-acetamidoimidazoles.
Bioorg.Med.Chem.Lett. 18 2062 2066 (2008)
PMID: 18291642 DOI: 10.1016/j.bmcl.2008.01.098

Abstact

Guided by X-ray crystallography of thrombin-inhibitor complexes and molecular modeling, alkylation of the N1 nitrogen of the imidazole P1 ligand of the pyridinoneacetamide thrombin inhibitor 1 with various acetamide moieties furnished inhibitors with significantly improved thrombin potency, trypsin selectivity, functional in vitro anticoagulant potency and in vivo antithrombotic efficacy. In the pyrazinoneacetamide series, oral bioavailability was also improved.

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Primary Citation of related structures
3C1K