3CSO

HCV Polymerase in complex with a 1,5 Benzodiazepine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

1,5-benzodiazepines, a novel class of hepatitis C virus polymerase nonnucleoside inhibitors.

Nyanguile, O.Pauwels, F.Van den Broeck, W.Boutton, C.W.Quirynen, L.Ivens, T.van der Helm, L.Vandercruyssen, G.Mostmans, W.Delouvroy, F.Dehertogh, P.Cummings, M.D.Bonfanti, J.F.Simmen, K.A.Raboisson, P.

(2008) Antimicrob.Agents Chemother. 52: 4420-4431

  • DOI: 10.1128/AAC.00669-08

  • PubMed Abstract: 
  • The exogenous control of hepatitis C virus (HCV) replication can be mediated through the inhibition of the RNA-dependent RNA polymerase (RdRp) activity of NS5B. Small-molecule inhibitors of NS5B include nucleoside and nonnucleoside analogs. Here, we ...

    The exogenous control of hepatitis C virus (HCV) replication can be mediated through the inhibition of the RNA-dependent RNA polymerase (RdRp) activity of NS5B. Small-molecule inhibitors of NS5B include nucleoside and nonnucleoside analogs. Here, we report the discovery of a novel class of HCV polymerase nonnucleoside inhibitors, 1,5-benzodiazepines (1,5-BZDs), identified by high-throughput screening of a library of small molecules. A fluorescence-quenching assay and X-ray crystallography revealed that 1,5-BZD 4a bound stereospecifically to NS5B next to the catalytic site. When introduced into replicons, mutations known to confer resistance against chemotypes that bind at this site were detrimental to inhibition by 1,5-BZD 7a. Using a panel of enzyme isolates that covered genotypes 1 to 6, we showed that compound 4a inhibited genotype 1 only. In mechanistic studies, 4a was found to inhibit the RdRp activity of NS5B noncompetitively with GTP and to inhibit the formation of the first phosphodiester bond during the polymerization cycle. The specificity for the HCV target was evaluated by profiling the 1,5-BZDs against other viral and human polymerases, as well as BZD receptors.


    Organizational Affiliation

    Tibotec BVBA, Generaal de Wittelaan L11B 3, 2800 Mechelen, Belgium. onyangui@its.jnj.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
581Hepatitis 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XNI
Query on XNI

Download SDF File 
Download CCD File 
A, B
(11S)-10-acetyl-11-[4-(benzyloxy)-3-chlorophenyl]-3,3-dimethyl-2,3,4,5,10,11-hexahydro-1H-dibenzo[b,e][1,4]diazepin-1-one
C30 H29 Cl N2 O3
KYABFOTZZRQAMR-LJAQVGFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XNIKi: 1700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.962α = 90.00
b = 108.224β = 90.00
c = 133.304γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Mol.phasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-10 
  • Released Date: 2009-04-14 
  • Deposition Author(s): Nyanguile, O.

Revision History 

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description