1OS5

Crystal structure of HCV NS5B RNA polymerase complexed with a novel non-competitive inhibitor.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme.

Love, R.A., Parge, H.E., Yu, X., Hickey, M.J., Diehl, W., Gao, J., Wriggers, H., Ekker, A., Wang, L., Thomson, J.A., Dragovich, P.S., Fuhrman, S.A.

(2003) J.Virol. 77: 7575-7581

  • DOI: 10.1128/jvi.77.13.7575-7581.2003

  • PubMed Abstract: 

    • The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has ...

    The virus-encoded nonstructural protein 5B (NS5B) of hepatitis C virus (HCV) is an RNA-dependent RNA polymerase and is absolutely required for replication of the virus. NS5B exhibits significant differences from cellular polymerases and therefore has become an attractive target for anti-HCV therapy. Using a high-throughput screen, we discovered a novel NS5B inhibitor that binds to the enzyme noncompetitively with respect to nucleotide substrates. Here we report the crystal structure of NS5B complexed with this small molecule inhibitor. Unexpectedly, the inhibitor is bound within a narrow cleft on the protein's surface in the "thumb" domain, about 30 A from the enzyme's catalytic center. The interaction between this inhibitor and NS5B occurs without dramatic changes to the structure of the protein, and sequence analysis suggests that the binding site is conserved across known HCV genotypes. Possible mechanisms of inhibition include perturbation of protein dynamics, interference with RNA binding, and disruption of enzyme oligomerization.

    Related Citations: 
    • Hepatitis C Virus (HCV) NS5B RNA Polymerase and Mutants Thereof.
      Love, R.A.,Parge, H.E.,Hickey, M.J.,Yu, X.,Fuhrman, S.A.,Diehl, W.,Gao, J.
      (2002) European Patent Application EP 1256628 --: --

    Organizational Affiliation: 

    Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. robert.love@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatitis C virus NS5B RNA polymerase
A
576Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 3 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NH1
Query on NH1
Download SDF File 
Download CCD File 
A
3-(4-AMINO-2-TERT-BUTYL-5-METHYL-PHENYLSULFANYL)-6-CYCLOPENTYL-4-HYDROXY-6-[2-(4-HYDROXY-PHENYL)-ETHYL]-5,6-DIHYDRO-PYRAN-2-ONE
C29 H37 N O4 S
ZEBFKFGJWHOOST-LJAQVGFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NH1Kd: 140 nM BINDINGMOAD
NH1Kd: 140 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.000α = 90.00
b = 83.000β = 90.00
c = 180.000γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance