3VQS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1128/AAC.00312-12

  • 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 nanomola ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B, C, D
578Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 0 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
JT1
Query on JT1

Download SDF File 
Download CCD File 
A, B, C, D
(2R)-4-(5-cyclopropyl[1,3]thiazolo[4,5-d]pyrimidin-2-yl)-N-[3-fluoro-4-(trifluoromethoxy)benzyl]-1-{[4-(trifluoromethyl)phenyl]sulfonyl}piperazine-2-carboxamide
C28 H23 F7 N6 O4 S2
JQLOVYLALGSISI-HXUWFJFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JT1IC50: 17.8 nM BINDINGMOAD
JT1IC50: 17.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 101.120α = 90.00
b = 101.180β = 90.00
c = 250.060γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-08
    Type: Initial release