4OK5

Crystal Structure of Hepatitis C Virus NS3 Helicase Inhibitor Co-complex with Compound 9 [1-(3-ethynylbenzyl)-1H-indol-3-yl]acetic acid]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/jm401432c
  • Primary Citation of Related Structures:  

  • 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. ...

    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, Qu├ębec H7S 2G5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease NS3
A, B
464Hepacivirus CMutation(s): 0 
Find proteins for K4KA16 (Hepacivirus C)
Go to UniProtKB:  K4KA16
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2T2
Query on 2T2

Download SDF File 
Download CCD File 
A
[1-(3-ethynylbenzyl)-1H-indol-3-yl]acetic acid
C19 H15 N O2
WFNGIMUEXODKKQ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2T2IC50: 31000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 81.797α = 90.00
b = 103.893β = 90.00
c = 118.474γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata reduction
PHENIXrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-01-21 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Padyana, A.K.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references