Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-cyclopropyl-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide

Experimental Data Snapshot

  • Resolution: 2.14 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase.

Gentles, R.G.Sheriff, S.Beno, B.R.Wan, C.Kish, K.Ding, M.Zheng, X.Chupak, L.Poss, M.A.Witmer, M.R.Morin, P.Wang, Y.K.Rigat, K.Lemm, J.Voss, S.Liu, M.Pelosi, L.Roberts, S.B.Gao, M.Kadow, J.F.

(2011) Bioorg Med Chem Lett 21: 2212-2215

  • DOI: https://doi.org/10.1016/j.bmcl.2011.03.011
  • Primary Citation of Related Structures:  
    3QGD, 3QGE, 3QGF, 3QGG, 3QGH, 3QGI

  • PubMed Abstract: 

    Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

  • Organizational Affiliation

    Bristol Myers Squibb, Chemical and Protein Technologies, Wallingford, CT 06492, United States. robert.gentles@bms.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase571hepatitis C virus genotype 1aMutation(s): 0 
Gene Names: NS5B
Find proteins for P26664 (Hepatitis C virus genotype 1a (isolate 1))
Explore P26664 
Go to UniProtKB:  P26664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26664
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.14 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.3α = 90
b = 84.7β = 90
c = 132.9γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2011-04-20 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description