Crystal structure of HCV NS5b 1b with (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyrimidine derivative

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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This is version 1.1 of the entry. See complete history


HCV NS5B polymerase inhibitors 2: Synthesis and in vitro activity of (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives.

Wang, G.Lei, H.Wang, X.Das, D.Hong, J.Mackinnon, C.H.Coulter, T.S.Montalbetti, C.A.Mears, R.Gai, X.Bailey, S.E.Ruhrmund, D.Hooi, L.Misialek, S.Rajagopalan, P.T.Cheng, R.K.Barker, J.J.Felicetti, B.Schonfeld, D.L.Stoycheva, A.Buckman, B.O.Kossen, K.Seiwert, S.D.Beigelman, L.

(2009) Bioorg Med Chem Lett 19: 4480-4483

  • DOI: 10.1016/j.bmcl.2009.05.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • (1,1-Dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives have been investigated as potential anti-HCV drugs. Their synthesis, HCV NS5B polymerase inhibition, and replicon activity are discussed.

    Organizational Affiliation

    Discovery Research, InterMune, Inc., Brisbane, CA 94005, USA. gyiwang@yahoo.com

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B576Hepatitis C virus (isolate BK)Mutation(s): 0 
EC: (PDB Primary Data), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt)
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B5P (Subject of Investigation/LOI)
Query on B5P

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]N-{3-[5-hydroxy-8-(3-methylbutyl)-7-oxo-7,8-dihydroimidazo[1,2-a]pyrimidin-6-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide
C19 H22 N6 O6 S2
 Ligand Interaction
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]GLYCEROL
C3 H8 O3
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B5P Binding MOAD:  3H98 IC50: 5 (nM) from 1 assay(s)
PDBBind:  3H98 IC50: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.931α = 90
b = 106.196β = 90
c = 126.417γ = 90
Software Package:
Software NamePurpose
DNAdata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment  

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance