2GDE image
Deposition Date 2006-03-16
Release Date 2007-03-20
Last Version Date 2024-11-06
Entry Detail
PDB ID:
2GDE
Title:
Thrombin in complex with inhibitor
Biological Source:
Source Organism(s):
Hirudo medicinalis (Taxon ID: 6421)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hirudin
Chain IDs:C (auth: D)
Chain Length:10
Number of Molecules:1
Biological Source:Hirudo medicinalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Thrombin heavy chain
Gene (Uniprot):F2
Chain IDs:B (auth: H)
Chain Length:259
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Thrombin light chain
Gene (Uniprot):F2
Chain IDs:A (auth: L)
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TYS C TYR O-SULFO-L-TYROSINE
Primary Citation
Total synthesis and structural confirmation of chlorodysinosin A.
J.Am.Chem.Soc. 128 10491 10495 (2006)
PMID: 16895415 DOI: 10.1021/ja0625834

Abstact

The first enantiocontrolled total synthesis of the marine sponge metabolite chlorodysinosin A is described. The structure and absolute configuration are identical to those of dysinosin A except for the presence of a novel 2S,3R-3-chloroleucine residue in the former. A concise stereocontrolled synthesis of the new chlorine-containing amino acid fragment was developed. An X-ray cocrystal structure of synthetic chlorodysinosin A with the enzyme thrombin confirms the structure and configuration assignment achieved through total synthesis. Within the aeruginosin family of natural products, chlorodysinosin A is the most potent inhibitor of the serine proteases thrombin, factor VIIa, and factor Xa, which are critical enzymes in the process leading to platelet aggregation and fibrin mesh formation in humans.

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Primary Citation of related structures
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