CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structure-Property Basis for Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in HCV NS5B Inhibitors.

Yeung, K.S.Beno, B.R.Mosure, K.Zhu, J.Grant-Young, K.A.Parcella, K.Anjanappa, P.Bora, R.O.Selvakumar, K.Wang, Y.K.Fang, H.Krause, R.Rigat, K.Liu, M.Lemm, J.Sheriff, S.Witmer, M.Tredup, J.Jardel, A.Kish, K.Parker, D.Haskell, R.Santone, K.Meanwell, N.A.Soars, M.G.Roberts, S.B.Kadow, J.F.

(2018) ACS Med Chem Lett 9: 1217-1222

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00379
  • Primary Citation of Related Structures:  
    5QJ0, 5QJ1

  • PubMed Abstract: 

    In solving the P-gp and BCRP transporter-mediated efflux issue in a series of benzofuran-derived pan-genotypic palm site inhibitors of the hepatitis C virus NS5B replicase, it was found that close attention to physicochemical properties was essential. In these compounds, where both molecular weight (MW >579) and TPSA (>110 Å 2 ) were high, attenuation of polar surface area together with weakening of hydrogen bond acceptor strength of the molecule provided a higher intrinsic membrane permeability and more desirable Caco-2 parameters, as demonstrated by trifluoroacetamide 11 and the benchmark N -ethylamino analog 12 . In addition, the tendency of these inhibitors to form intramolecular hydrogen bonds potentially contributes favorably to the improved membrane permeability and absorption. The functional group minimization that resolved the efflux problem simultaneously maintained potent inhibitory activity toward a gt-2 HCV replicon due to a switching of the role of substituents in interacting with the Gln414 binding pocket, as observed in gt-2a NS5B/inhibitor complex cocrystal structures, thus increasing the efficiency of the optimization. Noteworthy, a novel intermolecular S=O···C=O n → π* type interaction between the ligand sulfonamide oxygen atom and the carbonyl moiety of the side chain of Gln414 was observed. The insights from these structure-property studies and crystallography information provided a direction for optimization in a campaign to identify second generation pan-genotypic NS5B inhibitors.

  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-dependent RNA polymerase574Hepacivirus hominisMutation(s): 1 
EC: (PDB Primary Data), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt)
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1))
Explore Q99IB8 
Go to UniProtKB:  Q99IB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99IB8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on J6J

Download Ideal Coordinates CCD File 
B [auth A]6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide
C33 H29 F2 N5 O4
Query on PG4

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
S [auth A]
C8 H18 O5
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
P [auth A]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.44α = 90
b = 116.55β = 90
c = 64.71γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-11-21 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2021-05-12
    Changes: Structure summary