1RIW

Thrombin in complex with natural product inhibitor Oscillarin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin

Hanessian, S.Tremblay, M.Petersen, J.F.W.

(2004) J.Am.Chem.Soc. 126: 6064-6071

  • DOI: 10.1021/ja030669g

  • PubMed Abstract: 
  • 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 inc ...

    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.


    Organizational Affiliation

    Department of Chemistry, Université de Montréal, C.P. 6128, Station Centre-ville, Montréal, P.Q., H3C 3J7 Canada. stephen.hanessian@umontreal.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thrombin light chain
A
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
thrombin heavy chain, B
B
147Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
thrombin heavy chain, C
C
105Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Hirudin IIB
D
11Hirudo medicinalisMutation(s): 0 
Find proteins for P28506 (Hirudo medicinalis)
Go to UniProtKB:  P28506
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
OSC
Query on OSC

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Download CCD File 
C
(2R,3AS,6R,7AS)-N-(2-{1-[AMINO(IMINO)METHYL]-2,5-DIHYDRO-1H-PYRROL-3-YL}ETHYL)-6-HYDROXY-1-{N-[(2S)-2-HYDROXY-3-PHENYLPROPANOYL]PHENYLALANYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE
OSCILLARIN, (2R,3AS,6R,7AS)-6-HYDROXY-1-{(2R)-2-[(2R)-2-HYDROXY-3-PHENYL-PROPIONYLAMINO]-3-PHENYL-PROPIONYL}-OCTAHYDORO-INDOLE-2-CARBOXYLIC ACID [2-(1-CARBAMIMIDOYL-2,5-DIHYDRO-1H-PYRROL-3-YL)-ETHYL]-AMIDE
C34 H44 N6 O5
YNAKQOCSOOKXJP-VCNFNBSBSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
D
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OSCIC50: 28 nM BINDINGMOAD
OSCIC50: 28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.055α = 90.00
b = 72.366β = 100.19
c = 70.830γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
CCP4data scaling
MOSFLMdata reduction
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2013-03-13
    Type: Other