3D5M

Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2008.05.083
  • Primary Citation of Related Structures:  

  • 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 pote ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A, B
578Hepatitis C virus genotype 1b (isolate BK)Mutation(s): 1 
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4MS
Query on 4MS

Download SDF File 
Download CCD File 
A, 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-benzisothiazol-7-yl}methyl)methanesulfonamide
N-{3-[5-tert-Butyl-1-(3-chloro-4-fluoro-benzyl)-4-hydroxy-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]-1,1-dioxo-1H-1lambda6-benzo[d]isothiazol-7-ylmethyl}-methanesulfonamide
C24 H25 Cl F N3 O6 S2
OOHPVZYDADHCHM-JOCHJYFZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4MSIC50: <10 nM BINDINGMOAD
4MSIC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.304α = 90.00
b = 106.765β = 90.00
c = 126.254γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
EPMRphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance