5PZP

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 4-FLUORO-2-(4-FLUOROPHENYL)-N-METHYL-5-(2-METHYL-5-{[1-(PYRIMIDIN-2-YL)CYCLOPROPYL]CARBAMOYL}PHENYL)-1-BENZOFURAN-3-CARBOXAMIDE (BMS-929075)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Hepatitis C Virus NS5B Replicase Palm Site Allosteric Inhibitor (BMS-929075) Advanced to Phase 1 Clinical Studies.

Yeung, K.S.Beno, B.R.Parcella, K.Bender, J.A.Grant-Young, K.A.Nickel, A.Gunaga, P.Anjanappa, P.Bora, R.O.Selvakumar, K.Rigat, K.Wang, Y.K.Liu, M.Lemm, J.Mosure, K.Sheriff, S.Wan, C.Witmer, M.Kish, K.Hanumegowda, U.Zhuo, X.Shu, Y.Z.Parker, D.Haskell, R.Ng, A.Gao, Q.Colston, E.Raybon, J.Grasela, D.M.Santone, K.Gao, M.Meanwell, N.A.Sinz, M.Soars, M.G.Knipe, J.O.Roberts, S.B.Kadow, J.F.

(2017) J. Med. Chem. 60: 4369-4385

  • DOI: 10.1021/acs.jmedchem.7b00328
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hepatitis C virus (HCV) NS5B replicase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Inspired by the overlay of bound structures of three structurally distinct NS5B palm site al ...

    The hepatitis C virus (HCV) NS5B replicase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Inspired by the overlay of bound structures of three structurally distinct NS5B palm site allosteric inhibitors, the high-throughput screening hit anthranilic acid 4, the known benzofuran analogue 5, and the benzothiadiazine derivative 6, an optimization process utilizing the simple benzofuran template 7 as a starting point for a fragment growing approach was pursued. A delicate balance of molecular properties achieved via disciplined lipophilicity changes was essential to achieve both high affinity binding and a stringent targeted absorption, distribution, metabolism, and excretion profile. These efforts led to the discovery of BMS-929075 (37), which maintained ligand efficiency relative to early leads, demonstrated efficacy in a triple combination regimen in HCV replicon cells, and exhibited consistently high oral bioavailability and pharmacokinetic parameters across preclinical animal species. The human PK properties from the Phase I clinical studies of 37 were better than anticipated and suggest promising potential for QD administration.


    Organizational Affiliation

    Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
574Hepatitis C virus genotype 1b (isolate Con1)Mutation(s): 0 
Find proteins for Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Go to UniProtKB:  Q9WMX2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8XJ
Query on 8XJ

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Download CCD File 
A, B
4-fluoro-2-(4-fluorophenyl)-N-methyl-5-(2-methyl-5-{[1-(pyrimidin-2-yl)cyclopropyl]carbamoyl}phenyl)-1-benzofuran-3-carboxamide
C31 H24 F2 N4 O3
LZAUGCMVNLZVJV-UHFFFAOYSA-N
 Ligand Interaction
23E
Query on 23E

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Download CCD File 
A, B
(2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid
C38 H38 N4 O5
HDBNVTWMHMMKNY-XMHGGMMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.200α = 90.00
b = 90.700β = 90.00
c = 234.900γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
BUSTERrefinement
HKL-2000data reduction
HKL-2000data collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-27 
  • Released Date: 2017-05-10 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2018-02-21
    Type: Structure summary