5QJ0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/acsmedchemlett.8b00379
  • Primary Citation of Related Structures:  

  • 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 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.,Bristol-Myers Squibb Research and Development, P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States.,Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center, Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
A
574Hepatitis C virus genotype 2a (isolate JFH-1)Mutation(s): 1 
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1))
Go to UniProtKB:  Q99IB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2PE
Query on 2PE

Download SDF File 
Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
J6D
Query on J6D

Download SDF File 
Download CCD File 
A
6-[ethyl(methylsulfonyl)amino]-2-(4-fluorophenyl)-N-methyl-5-(3-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide
C33 H30 F N5 O5 S
AWFOIGBVORNGMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.250α = 90.00
b = 89.986β = 90.00
c = 124.090γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTERrefinement
AMoREphasing
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-08-13 
  • Released Date: 2018-11-21 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references