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: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    2WHO

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEAB536Hepatitis C virus (isolate BK)Mutation(s): 0 
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)
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGI
Query on VGI

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
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGIIC50:  1000   nM  BindingDB
VGIIC50 :  20   nM  PDBBind
VGIIC50:  20   nM  BindingDB
VGIEC50:  7100   nM  BindingDB
VGIIC50:  20   nM  Binding MOAD
VGIIC50:  500   nM  BindingDB
VGIIC50:  20   nM  BindingDB
VGIIC50:  64   nM  BindingDB
VGIIC50:  78   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.21α = 90
b = 96.999β = 90
c = 193.762γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-01-23
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary