Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Structure-based design, synthesis, and biological evaluation of 1,1-dioxoisothiazole and benzo[b]thiophene-1,1-dioxide derivatives as novel inhibitors of hepatitis C virus NS5B polymerase.

Kim, S.H.Tran, M.T.Ruebsam, F.Xiang, A.X.Ayida, B.McGuire, H.Ellis, D.Blazel, J.Tran, C.V.Murphy, D.E.Webber, S.E.Zhou, Y.Shah, A.M.Tsan, M.Showalter, R.E.Patel, R.Gobbi, A.LeBrun, L.A.Bartkowski, D.M.Nolan, T.G.Norris, D.A.Sergeeva, M.V.Kirkovsky, L.Zhao, Q.Han, Q.Kissinger, C.R.

(2008) Bioorg Med Chem Lett 18: 4181-4185

  • DOI: https://doi.org/10.1016/j.bmcl.2008.05.083
  • Primary Citation of Related Structures:  
    3D28, 3D5M

  • PubMed Abstract: 

    A novel series of HCV NS5B polymerase inhibitors comprising 1,1-dioxoisothiazoles and benzo[b]thiophene-1,1-dioxides were designed, synthesized, and evaluated. SAR studies guided by structure-based design led to the identification of a number of potent NS5B inhibitors with nanomolar IC(50) values. The most potent compound exhibited IC(50) less than 10nM against the genotype 1b HCV polymerase and EC(50) of 70 nM against a genotype 1b replicon in cell culture. The DMPK properties of selected compounds were also evaluated.

  • Organizational Affiliation

    Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA. sdsunhee@yahoo.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase
A, B
578Hepatitis C virus (isolate BK)Mutation(s): 1 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4MS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-({3-[(5S)-5-tert-butyl-1-(3-chloro-4-fluorobenzyl)-4-hydroxy-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]-1,1-dioxido-1,2-benzis othiazol-7-yl}methyl)methanesulfonamide
C24 H25 Cl F N3 O6 S2
Binding Affinity Annotations 
IDSourceBinding Affinity
4MS PDBBind:  3D5M IC50: 10 (nM) from 1 assay(s)
Binding MOAD:  3D5M IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.304α = 90
b = 106.765β = 90
c = 126.254γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data 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: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary