3VQS | pdb_00003vqs

Crystal structure of HCV NS5B RNA polymerase with a novel piperazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Preclinical Characterization of JTK-853, a Novel Nonnucleoside Inhibitor of the Hepatitis C Virus RNA-Dependent RNA Polymerase.

Ando, I.Adachi, T.Ogura, N.Toyonaga, Y.Sugimoto, K.Abe, H.Kamada, M.Noguchi, T.

(2012) Antimicrob Agents Chemother 56: 4250-4256

  • DOI: https://doi.org/10.1128/AAC.00312-12
  • Primary Citation Related Structures: 
    3VQS

  • PubMed Abstract: 

    JTK-853 is a novel piperazine derivative nonnucleoside inhibitor of hepatitis C virus (HCV) RNA-dependent RNA polymerase. JTK-853 showed potent inhibitory activity against genotype 1 HCV polymerase, with a 50% inhibitory concentration in the nanomolar range, and showed potent antiviral activity against the genotype 1b replicon, with a 50% effective concentration of 0.035 μM. The presence of human serum at up to 40% had little effect on the antiviral activity of JTK-853. Structure analysis of HCV polymerase with JTK-853 revealed that JTK-853 associates with the palm site and β-hairpin region of HCV polymerase, and JTK-853 showed decreased antiviral activity against HCV replicons bearing the resistance mutations C316Y, M414T, Y452H, and L466V in the palm site region of HCV polymerase. JTK-853 showed an additive combination effect with other DAAs (direct antiviral agents), such as nucleoside polymerase inhibitor, thumb pocket-binding nonnucleoside polymerase inhibitor, NS5A inhibitor, and protease inhibitor. Collectively, these data demonstrate that JTK-853 is a potent and novel nonnucleoside palm site-binding HCV polymerase inhibitor, suggesting JTK-853 as a potentially useful agent in combination with other DAAs for treatment of HCV infections.


  • Organizational Affiliation
    • Central Pharmaceutical Research Institute, Japan Tobacco, Inc., Takatsuki, Osaka, Japan.

Macromolecule Content 

  • Total Structure Weight: 259.88 kDa 
  • Atom Count: 19,445 
  • Modeled Residue Count: 2,219 
  • Deposited Residue Count: 2,312 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase
A, B, C, D
578Orthohepacivirus hominisMutation(s): 0 
Gene Names: genotype 1b
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.204 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.12α = 90
b = 101.18β = 90
c = 250.06γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary