1RIW image
Deposition Date 2003-11-18
Release Date 2004-11-09
Last Version Date 2024-12-25
Entry Detail
PDB ID:
1RIW
Title:
Thrombin in complex with natural product inhibitor Oscillarin
Biological Source:
Source Organism:
Hirudo medicinalis (Taxon ID: 6421)
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.04 Å
R-Value Free:
0.23
R-Value Work:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:thrombin light chain
Gene (Uniprot):F2
Chain IDs:A
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:thrombin heavy chain, B
Gene (Uniprot):F2
Chain IDs:B
Chain Length:147
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:thrombin heavy chain, C
Gene (Uniprot):F2
Chain IDs:C
Chain Length:105
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Hirudin IIB
Chain IDs:D
Chain Length:11
Number of Molecules:1
Biological Source:Hirudo medicinalis
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN B ASN GLYCOSYLATION SITE
TYS D TYR O-SULFO-L-TYROSINE
Primary Citation
The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin
J.Am.Chem.Soc. 126 6064 6071 (2004)
PMID: 15137772 DOI: 10.1021/ja030669g

Abstact

The first enantiocontrolled total synthesis of the marine natural product oscillarin is described. The proposed structure and absolute configuration of oscillarin is thus confirmed, and a previously assigned structure of a subunit was shown to be incorrect. The X-ray structure of an oscillarin-thrombin complex was resolved at 2.0 A resolution, which validated its potent inhibitory activity against the enzyme with an IC(50) = 28 nM. Methodology was developed for the synthesis of enantiopure octahydroindole-2-carboxylic acids with usable functionality at C-6. The method consists of the halocarbocyclization of N-acyloxyiminium ions containing an olefinic tether in the presence of tin tetrachloride or tin tetrabromide. This N-acyloxyiminium ion aza-Prins carbocyclization proved to be general for the construction of octahydroindole and perhydroquinoline 2-carboxylic acids. Mechanistic rationales are based on an antiperiplanar attack of the terminal alkene on the iminium ion, leading to an incipient secondary carbocation which is trapped by halide via an equatorial attack. X-ray crystal structures of products corroborate the expected stereochemistry.

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Primary Citation of related structures