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 
  • R-Value Observed: 0.183 

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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
  • Primary Citation of Related Structures:  
    3CSO

  • 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 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B581Hepatitis C virus isolate HC-J4Mutation(s): 0 
Gene Names: HCV-NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for O92972 (Hepatitis C virus genotype 1b (strain HC-J4))
Explore O92972 
Go to UniProtKB:  O92972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO92972
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XNI
Query on XNI
Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
XNI PDBBind:  3CSO Ki: 1700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.962α = 90
b = 108.224β = 90
c = 133.304γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
Mol.phasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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