Structure of the genotype 2B HCV polymerase bound to a NNI

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


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.Antenni, B.Melancona, 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.

To be published.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Genome polyproteinA, B563Hepatitis C virus isolate HC-J8Mutation(s): 1 
EC: (PDB Primary Data), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt)
Find proteins for P26661 (Hepatitis C virus genotype 2b (isolate HC-J8))
Explore P26661 
Go to UniProtKB:  P26661
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26661
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on VGI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H15 Br N2 O3
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VGI BindingDB:  3HVO IC50: min: 180, max: 770 (nM) from 2 assay(s)
EC50: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.293α = 90
b = 64.648β = 89.73
c = 135.714γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-01-23
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Derived calculations