2BDY image
Deposition Date 2005-10-21
Release Date 2006-10-24
Last Version Date 2024-11-20
Entry Detail
PDB ID:
2BDY
Keywords:
HYDROLASE/HYDROLASE INHIBITOR
Title:
thrombin in complex with inhibitor
Biological Source:
Source Organism:
Hirudo medicinalis (Taxon ID: 6421)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.61 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
2BDY validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Thrombin
Gene (Uniprot):F2
Chain IDs:A
Chain Length:289
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P00734 Pfam ID:PF09396, PF00089 EC:3.4.21.5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hirudin IIIB'
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:Hirudo medicinalis
UniProt ID:P01050
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TYS B TYR O-SULFO-L-TYROSINE
Ligand Molecules
NA
UNB
Primary Citation
Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.
Bioorg.Med.Chem.Lett. 16 1032 1036 (2006)
PMID: 16290930 DOI: 10.1016/j.bmcl.2005.10.082

Abstact

Prototypical thrombin inhibitors were synthesized based on a trisubstituted phenol as a core motif. A naphthylsulfonamide analogue showed excellent antithrombin activity. An X-ray co-crystal structure showed the expected interactions.

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Protein

Chemical

Disease

Primary Citation of related structures
2BDY