2WCX | pdb_00002wcx

Crystal Structure of Hepatitis C Virus NS5B Polymerase in Complex with Thienopyrrole-Based Finger-Loop Inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.209 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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Literature

Optimization of Thienopyrrole-Based Finger-Loop Inhibitors of the Hepatitis C Virus Ns5B Polymerase.

Martin Hernando, J.I., Ontoria, J.M., Malancona, S., Attenni, B., Fiore, F., Bonelli, F., Koch, U., Di Marco, S., Colarusso, S., Ponzi, S., Gennari, N., Vignetti, S.E., Del Rosario Rico Ferreira, M., Habermann, J., Rowley, M., Narjes, F.

(2009) ChemMedChem 4: 1695

  • DOI: https://doi.org/10.1002/cmdc.200900184
  • Primary Citation Related Structures: 
    2WCX

  • PubMed Abstract: 

    Infections caused by the hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. The NS5B polymerase of HCV is responsible for the replication of viral RNA and has been a prime target in the search for novel treatment options. We had discovered allosteric finger-loop inhibitors based on a thieno[3,2-b]pyrrole scaffold as an alternative to the related indole inhibitors. Optimization of the thienopyrrole series led to several N-acetamides with submicromolar potency in the cell-based replicon assay, but they lacked oral bioavailability in rats. By linking the N4-position to the ortho-position of the C5-aryl group, we were able to identify the tetracyclic thienopyrrole 40, which displayed a favorable pharmacokinetic profile in rats and dogs and is equipotent with recently disclosed finger-loop inhibitors based on an indole scaffold.

    • Organizational Affiliation: 
    • Department of Medicinal Chemistry, Istituto di Ricerche di Biologia Molecolare P. Angeletti S.p.A. Merck Sharp & Dohme Research Laboratories Rome, Via Pontina km 30,600, 00040 Pomezia (Italy).

Macromolecule Content 

  • Total Structure Weight: 60.22 kDa 
  • Atom Count: 4,511 
  • Modeled Residue Count: 512 
  • Deposited Residue Count: 537 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASE537Hepatitis C virus (isolate BK)Mutation(s): 0 
EC: 2.7.7.48
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.209 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.407α = 90
b = 94.708β = 90
c = 95.54γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2009-08-18 
    • Deposition Author(s): Di Marco, S.

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-11-23
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description