3D5M | pdb_00003d5m

Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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 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

Macromolecule Content 

  • Total Structure Weight: 129.83 kDa 
  • Atom Count: 9,072 
  • Modeled Residue Count: 1,116 
  • Deposited Residue Count: 1,156 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase
A, B
578Hepatitis C virus (isolate BK)Mutation(s): 1 
EC: 2.7.7.48
UniProt
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4MS

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
OOHPVZYDADHCHM-JOCHJYFZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
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
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing

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
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary