5TWM

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase.

Eastman, K.J.Parcella, K.Yeung, K.S.Grant-Young, K.A.Zhu, J.Wang, T.Zhang, Z.Yin, Z.Beno, B.R.Sheriff, S.Kish, K.Tredup, J.Jardel, A.G.Halan, V.Ghosh, K.Parker, D.Mosure, K.Fang, H.Wang, Y.K.Lemm, J.Zhuo, X.Hanumegowda, U.Rigat, K.Donoso, M.Tuttle, M.Zvyaga, T.Haarhoff, Z.Meanwell, N.A.Soars, M.G.Roberts, S.B.Kadow, J.F.

(2017) Medchemcomm 8: 796-806

  • DOI: 10.1039/c6md00636a
  • Primary Citation of Related Structures:  
    5TWM, 5TWN

  • PubMed Abstract: 
  • The development of a series of novel 7-azabenzofurans exhibiting pan-genotype inhibition of HCV NS5B polymerase via binding to the primer grip site is presented. Many challenges, including poor oral bioavailability, high clearance, bioactivation, high human serum shift, and metabolic stability were encountered and overcome through SAR studies ...

    The development of a series of novel 7-azabenzofurans exhibiting pan-genotype inhibition of HCV NS5B polymerase via binding to the primer grip site is presented. Many challenges, including poor oral bioavailability, high clearance, bioactivation, high human serum shift, and metabolic stability were encountered and overcome through SAR studies. This work culminated in the selection of BMS-986139 ( 43 ) as a preclinical candidate.


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research and Development , Department of Discovery Chemistry and Molecular Technologies , 5 Research Parkway , Wallingford , Connecticut , USA . Email: kyle.eastman@bms.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NS5B RNA-dependent RNA POLYMERASEA574Hepatitis C virus JFH-1Mutation(s): 1 
Gene Names: NS5B
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for Q99IB8 (Hepatitis C virus genotype 2a (isolate JFH-1))
Explore Q99IB8 
Go to UniProtKB:  Q99IB8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7NG (Subject of Investigation/LOI)
Query on 7NG

Download Ideal Coordinates CCD File 
B [auth A]5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide
C28 H29 F N4 O3
WDGCNGHMLOOKQZ-UHFFFAOYSA-N
 Ligand Interaction
PE5
Query on PE5

Download Ideal Coordinates CCD File 
G [auth A]3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A], I [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.687α = 90
b = 89.816β = 90
c = 216.745γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2016-11-14 
  • Released Date: 2017-03-15 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references