5PZO

CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE C316N IN COMPLEX WITH 2-(4-FLUOROPHENYL)-N-METHYL-5-[3-({2-METHYL-1-OXO-1-[(1,3,4-THIADIAZOL-2-YL)AMINO]PROPAN-2-YL}CARBAMOYL)PHENYL]-1-BENZOFURAN-3-CARBOXAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5PZK, 5PZL, 5PZM, 5PZN, 5PZO, 5PZP

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B574Hepatitis C virus (isolate Con1)Mutation(s): 1 
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 Q9WMX2 (Hepatitis C virus genotype 1b (isolate Con1))
Explore Q9WMX2 
Go to UniProtKB:  Q9WMX2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
23E (Subject of Investigation/LOI)
Query on 23E

Download Ideal Coordinates CCD File 
C [auth A], N [auth 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
8XM (Subject of Investigation/LOI)
Query on 8XM

Download Ideal Coordinates CCD File 
D [auth A], O [auth B]2-(4-fluorophenyl)-N-methyl-5-[3-({2-methyl-1-oxo-1-[(1,3,4-thiadiazol-2-yl)amino]propan-2-yl}carbamoyl)phenyl]-1-benzofuran-3-carboxamide
C29 H24 F N5 O4 S
XZMBOYQAHQFYNQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , T [auth B] , U [auth B] , V [auth B] , 
I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B], W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.2α = 90
b = 90.3β = 90
c = 234.9γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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