4OK3

Crystal Structure of Hepatitis C Virus NS3 Helicase Inhibitor Co-complex with Compound 7 [[1-(3-chlorobenzyl)-1H-indol-3-yl]acetic acid]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

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This is version 1.2 of the entry. See complete history


Literature

Integrated strategies for identifying leads that target the NS3 helicase of the hepatitis C virus.

Laplante, S.R.Padyana, A.K.Abeywardane, A.Bonneau, P.Cartier, M.Coulombe, R.Jakalian, A.Wildeson-Jones, J.Li, X.Liang, S.McKercher, G.White, P.Zhang, Q.Taylor, S.J.

(2014) J Med Chem 57: 2074-2090

  • DOI: https://doi.org/10.1021/jm401432c
  • Primary Citation of Related Structures:  
    4OJQ, 4OK3, 4OK5, 4OK6, 4OKS

  • PubMed Abstract: 

    Future treatments for individuals infected by the hepatitis C virus (HCV) will likely involve combinations of compounds that inhibit multiple viral targets. The helicase of HCV is an attractive target with no known drug candidates in clinical trials. Herein we describe an integrated strategy for identifying fragment inhibitors using structural and biophysical techniques. Based on an X-ray structure of apo HCV helicase and in silico and bioinformatic analyses of HCV variants, we identified that one site in particular (labeled 3 + 4) was the most conserved and attractive pocket to target for a drug discovery campaign. Compounds from multiple sources were screened to identify inhibitors or binders to this site, and enzymatic and biophysical assays (NMR and SPR) were used to triage the most promising ligands for 3D structure determination by X-ray crystallography. Medicinal chemistry and biophysical evaluations focused on exploring the most promising lead series. The strategies employed here can have general utility in drug discovery.


  • Organizational Affiliation

    Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd, R&D , 2100 Cunard Street, Laval, Québec H7S 2G5, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease NS3
A, B
464Hepacivirus hominisMutation(s): 0 
Gene Names: NS3
UniProt
Find proteins for K4KA16 (Hepacivirus hominis)
Explore K4KA16 
Go to UniProtKB:  K4KA16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4KA16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.394α = 90
b = 104.232β = 90
c = 117.954γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations