2WHO

CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE FROM 1B GENOTYPE IN COMPLEX WITH A NON-NUCLEOSIDE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors.

Ontoria, J.M.Rydberg, E.H.Di Marco, S.Tomei, L.Attenni, B.Malancona, S.Martin Hernando, J.I.Gennari, N.Koch, U.Narjes, F.Rowley, M.Summa, V.Carroll, S.S.Olsen, D.B.De Francesco, R.Altamura, S.Migliaccio, G.Carfi, A.

(2009) J. Med. Chem. 52: 5217-5227

  • DOI: 10.1021/jm900517t

  • PubMed Abstract: 
  • The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for inhibition. Herein, we present 1H- ...

    The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells and, as a consequence, is an attractive target for inhibition. Herein, we present 1H-benzo[de]isoquinoline-1,3(2H)-diones as a new series of selective inhibitors of HCV NS5B polymerase. The HTS hit 1 shows submicromolar potency in two different HCV replicons (1b and 2b) and displays no activity on other polymerases (HIV-RT, Polio-pol, GBV-b-pol). These inhibitors act during the pre-elongation phase by binding to NS5B non-nucleoside binding site Thumb Site II as demonstrated by crystal structure of compound 1 with the DeltaC55-1b and DeltaC21-2b enzymes and by mutagenesis studies. SAR in this new series reveals inhibitors, such as 20, with low micromolar activity in the HCV replicon and with good activity/toxicity window in cells.


    Organizational Affiliation

    Istituto Di Ricerche Di Biologia Molecolare, P. Angeletti, S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, I-00040 Pomezia, Italy. jesus_ontoria@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-DIRECTED RNA POLYMERASE
A, B
536Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 0 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
VGI
Query on VGI

Download SDF File 
Download CCD File 
A, B
2-(3-bromophenyl)-6-[(2-hydroxyethyl)amino]-1h-benzo[de]isoquinoline-1,3(2h)-dione
C20 H15 Br N2 O3
JZCUVYNOSDWORZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGIIC50: 20 - >1000 nM (100) BINDINGDB
VGIEC50: 7100 nM (100) BINDINGDB
VGIIC50: 20 nM BINDINGMOAD
VGIIC50: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.210α = 90.00
b = 96.999β = 90.00
c = 193.762γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-05-05 
  • Released Date: 2009-08-11 
  • Deposition Author(s): Di Marco, S.

Revision History 

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2019-01-23
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary