4JJU

Crystal structure of HCV NS5B polymerase in complex with COMPOUND 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design of novel HCV NS5B thumb pocket 2 allosteric inhibitors with submicromolar gt1 replicon potency: Discovery of a quinazolinone chemotype.

Beaulieu, P.L.Coulombe, R.Duan, J.Fazal, G.Godbout, C.Hucke, O.Jakalian, A.Joly, M.A.Lepage, O.Llinas-Brunet, M.Naud, J.Poirier, M.Rioux, N.Thavonekham, B.Kukolj, G.Stammers, T.A.

(2013) Bioorg.Med.Chem.Lett. 23: 4132-4140

  • DOI: 10.1016/j.bmcl.2013.05.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the structure-based design of a novel lead chemotype that binds to thumb pocket 2 of HCV NS5B polymerase and inhibits cell-based gt1 subgenomic reporter replicons at sub-micromolar concentrations (EC50<200nM). This new class of potent thu ...

    We describe the structure-based design of a novel lead chemotype that binds to thumb pocket 2 of HCV NS5B polymerase and inhibits cell-based gt1 subgenomic reporter replicons at sub-micromolar concentrations (EC50<200nM). This new class of potent thumb pocket 2 inhibitors features a 1H-quinazolin-4-one scaffold derived from hybridization of a previously reported, low affinity thiazolone chemotype with our recently described anthranilic acid series. Guided by X-ray structural information, a key NS5B-ligand interaction involving the carboxylate group of anthranilic acid based inhibitors was replaced by a neutral two-point hydrogen bonding interaction between the quinazolinone scaffold and the protein backbone. The in vitro ADME and in vivo rat PK profile of representative analogs are also presented and provide areas for future optimization of this new class of HCV polymerase inhibitors.


    Organizational Affiliation

    Medicinal Chemistry, Boehringer Ingelheim (Canada) Ltd, Research and Development, 2100 Cunard Street, Laval, Quebec H7S 2G5, Canada. resgeneral.lav@boehringer-ingelheim.com




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
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1MB
Query on 1MB

Download SDF File 
Download CCD File 
A, B
1-(2,4-difluorobenzyl)-6-{[3-(trifluoromethyl)pyridin-2-yl]oxy}quinazolin-4(1H)-one
C21 H12 F5 N3 O2
SWXDHFLZCMRYEP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1MBIC50: 510 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.070α = 90.00
b = 108.390β = 90.00
c = 134.880γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
CNXrefinement
XDSdata reduction
CNXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-03-08 
  • Released Date: 2013-06-12 
  • Deposition Author(s): Coulombe, R.

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description