4JTY

Crystal structure of HCV NS5B polymerase with COMPOUND 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Dynamics Simulations and Structure-Based Rational Design Lead to Allosteric HCV NS5B Polymerase Thumb Pocket 2 Inhibitor with Picomolar Cellular Replicon Potency.

Hucke, O.Coulombe, R.Bonneau, P.Bertrand-Laperle, M.Brochu, C.Gillard, J.Joly, M.A.Landry, S.Lepage, O.Llinas-Brunet, M.Pesant, M.Poirier, M.Poirier, M.McKercher, G.Marquis, M.Kukolj, G.Beaulieu, P.L.Stammers, T.A.

(2014) J.Med.Chem. 57: 1932-1943

  • DOI: 10.1021/jm4004522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The design and preliminary SAR of a new series of 1H-quinazolin-4-one (QAZ) allosteric HCV NS5B thumb pocket 2 (TP-2) inhibitors was recently reported. To support optimization efforts, a molecular dynamics (MD) based modeling workflow was implemented ...

    The design and preliminary SAR of a new series of 1H-quinazolin-4-one (QAZ) allosteric HCV NS5B thumb pocket 2 (TP-2) inhibitors was recently reported. To support optimization efforts, a molecular dynamics (MD) based modeling workflow was implemented, providing information on QAZ binding interactions with NS5B. This approach predicted a small but critical ligand-binding induced movement of a protein backbone region which increases the pocket size and improves access to the backbone carbonyl groups of Val 494 and Pro 495. This localized backbone shift was consistent with key SAR results and was subsequently confirmed by X-ray crystallography. The MD protocol guided the design of inhibitors, exploiting novel H-bond interactions with the two backbone carbonyl groups, leading to the first thumb pocket 2 NS5B inhibitor with picomolar antiviral potency in genotype (gt) 1a and 1b replicons (EC50 = 120 and 110 pM, respectively) and with EC50 ≤ 80 nM against gt 2-6.


    Organizational Affiliation

    Research and Development, Boehringer Ingelheim (Canada) Ltd. , 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Genome polyprotein
A, B
576Hepatitis C virus genotype 1b (strain HC-J4)Mutation(s): 0 
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Go to UniProtKB:  O92972
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
1NV
Query on 1NV

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Download CCD File 
A, B
3-{[4-oxo-1-(2,4,6-trifluorobenzyl)-1,4-dihydroquinazolin-6-yl]oxy}-2-(trifluoromethyl)benzamide
C23 H13 F6 N3 O3
UJEKCTGHTGBATO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.200α = 90.00
b = 107.570β = 90.00
c = 134.520γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata reduction
CNXrefinement
XDSdata scaling
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-24 
  • Released Date: 2013-07-03 
  • Deposition Author(s): Coulombe, R.

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references