4IZ0

Crystal structure of HCV NS5B polymerase in complex with 2,4,5-trichloro-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors.

Stammers, T.A.Coulombe, R.Rancourt, J.Thavonekham, B.Fazal, G.Goulet, S.Jakalian, A.Wernic, D.Tsantrizos, Y.Poupart, M.A.Bos, M.McKercher, G.Thauvette, L.Kukolj, G.Beaulieu, P.L.

(2013) Bioorg Med Chem Lett 23: 2585-2589

  • DOI: 10.1016/j.bmcl.2013.02.110
  • Primary Citation of Related Structures:  
    4J02, 4J04, 4J06, 4J08, 4J0A, 4IZ0

  • PubMed Abstract: 
  • A novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors were derived from a fragment-based approach using information from X-ray crystallographic analysis of NS5B-inhibitor complexes and iterative rounds of parallel synthesis. ...

    A novel series of non-nucleoside thumb pocket 2 HCV NS5B polymerase inhibitors were derived from a fragment-based approach using information from X-ray crystallographic analysis of NS5B-inhibitor complexes and iterative rounds of parallel synthesis. Structure-based drug design strategies led to the discovery of potent sub-micromolar inhibitors 11a-c and 12a-c from a weak-binding fragment-like structure 1 as a starting point.


    Organizational Affiliation

    Department of Chemistry, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 rue Cunard, Laval, Québec, Canada H7S 2G5. timothy.stammers@boehringer-ingelheim.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseAB576Hepatitis C virus isolate HC-J4Mutation(s): 0 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Explore O92972 
Go to UniProtKB:  O92972
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2BI
Query on 2BI

Download CCD File 
A
2,4,5-trichloro-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide
C10 H7 Cl3 N2 O3 S
HFFXLYHRNRKAPM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2BIIC50 :  100000   nM  PDBBind
2BIIC50:  100000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.71α = 90
b = 107.85β = 90
c = 133.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-01-29 
  • Released Date: 2013-04-17 
  • Deposition Author(s): Coulombe, R.

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release
  • Version 1.1: 2013-05-01
    Changes: Database references