3CDE

Crystal structure of HCV NS5B polymerase with a novel Pyridazinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 3: Further optimization of the 2-, 6-, and 7'-substituents and initial pharmacokinetic assessments.

Li, L.S.Zhou, Y.Murphy, D.E.Stankovic, N.Zhao, J.Dragovich, P.S.Bertolini, T.Sun, Z.Ayida, B.Tran, C.V.Ruebsam, F.Webber, S.E.Shah, A.M.Tsan, M.Showalter, R.E.Patel, R.Lebrun, L.A.Bartkowski, D.M.Nolan, T.G.Norris, D.A.Kamran, R.Brooks, J.Sergeeva, M.V.Kirkovsky, L.Zhao, Q.Kissinger, C.R.

(2008) Bioorg.Med.Chem.Lett. 18: 3446-3455

  • DOI: 10.1016/j.bmcl.2008.02.072

  • PubMed Abstract: 
  • 5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. Lead optimization led to the discovery of compound 3a, which displayed potent inhibitory activities in biochemical and replicon assays [IC(50) ...

    5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. Lead optimization led to the discovery of compound 3a, which displayed potent inhibitory activities in biochemical and replicon assays [IC(50) (1b)<10nM; IC(50) (1a)=22 nM; EC(50) (1b)=5nM], good stability toward human liver microsomes (HLM t(1/2)>60 min), and high ratios of liver to plasma concentrations 12h after a single oral administration to rats.


    Organizational Affiliation

    Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA.




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
N3H
Query on N3H

Download SDF File 
Download CCD File 
A, B
N-{3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide
N-{3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxo-2H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide
C21 H23 N5 O6 S3
UNKTYNIAIAATDF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N3HEC50: 5 nM (99) BINDINGDB
N3HIC50: <10 nM (99) BINDINGDB
N3HIC50: <10 nM BINDINGMOAD
N3HIC50: 22 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 85.637α = 90.00
b = 106.258β = 90.00
c = 126.930γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance