5W2E | pdb_00005w2e

HCV NS5B RNA-dependent RNA polymerase in complex with non-nucleoside inhibitor MK-8876


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.239 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Development of a New Structural Class of Broadly Acting HCV Non-Nucleoside Inhibitors Leading to the Discovery of MK-8876.

McComas, C.C.Palani, A.Chang, W.Holloway, M.K.Lesburg, C.A.Li, P.Liverton, N.Meinke, P.T.Olsen, D.B.Peng, X.Soll, R.M.Ummat, A.Wu, J.Wu, J.Zorn, N.Ludmerer, S.W.

(2017) ChemMedChem 12: 1436-1448

  • DOI: https://doi.org/10.1002/cmdc.201700228
  • Primary Citation Related Structures: 
    5W2E

  • PubMed Abstract: 

    Studies directed at developing a broadly acting non-nucleoside inhibitor of HCV NS5B led to the discovery of a novel structural class of 5-aryl benzofurans that simultaneously interact with both the palm I and palm II binding regions. An initial candidate was potent in vitro against HCV GT1a and GT1b replicons, and induced multi-log reductions in HCV viral load when orally dosed to chronic GT1 infected chimpanzees. However, in vitro potency losses against clinically relevant GT1a variants prompted a further effort to develop compounds with sustained potency across a broader array of HCV genotypes and mutants. Ultimately, a biology and medicinal chemistry collaboration led to the discovery of the development candidate MK-8876. MK-8876 demonstrated a pan-genotypic potency profile and maintained potency against clinically relevant mutants. It demonstrated moderate bioavailability in rats and dogs, but showed low plasma clearance characteristics consistent with once-daily dosing. Herein we describe the efforts which led to the discovery of MK-8876, which advanced into Phase 1 monotherapy studies for evaluation and characterization as a component of an all-oral direct-acting drug regimen for the treatment of chronic HCV infection.


  • Organizational Affiliation
    • Merck & Co. Inc., Kenilworth, NJ, USA.

Macromolecule Content 

  • Total Structure Weight: 129.37 kDa 
  • Atom Count: 9,052 
  • Modeled Residue Count: 1,118 
  • Deposited Residue Count: 1,152 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyprotein
A, B
576Hepatitis C virus (isolate BK)Mutation(s): 3 
EC: 3.4.22 (PDB Primary Data), 3.4.21.98 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26663
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9VY

Query on 9VY



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-(4-fluorophenyl)-5-(11-fluoro-6H-pyrido[2',3':5,6][1,3]oxazino[3,4-a]indol-2-yl)-N-methyl-6-[methyl(methylsulfonyl)amino]-1-benzofuran-3-carboxamide
C32 H24 F2 N4 O5 S
GOHCXBUFLQKEIO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.239 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.092α = 90
b = 106.418β = 90
c = 126.091γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description