3CWJ

Crystal structure of hcv ns5b polymerase with a novel pyridazinone inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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Literature

4-(1,1-Dioxo-1,4-dihydro-1lambda6-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-ones as potent inhibitors of HCV NS5B polymerase

Ellis, D.A., Blazel, J.K., Webber, S.E., Tran, C.V., Dragovich, P.S., Sun, Z., Ruebsam, F., McGuire, H.M., Xiang, A.X., Zhao, J., Li, L.S., Zhou, Y., Han, Q., Kissinger, C.R., Showalter, R.E., Lardy, M., Shah, A.M., Tsan, M., Patel, R., LeBrun, L.A., Kamran, R., Bartkowski, D.M., Nolan, T.G., Norris, D.A., Sergeeva, M.V., Kirkovsky, L.

(2008) Bioorg Med Chem Lett 18: 4628-4632

  • DOI: 10.1016/j.bmcl.2008.07.014
  • Primary Citation of Related Structures:  
    3CWJ

  • PubMed Abstract: 

    • 4-(1,1-Dioxo-1,4-dihydro-1lambda(6)-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-one analogs were discovered as a novel class of inhibitors of HCV NS5B polymerase. Structure-based design led to the identification of compound 3a that displayed potent inhibitory activities in biochemical and replicon assays (1b IC(50)<10 nM; 1b EC(50)=1 ...

    4-(1,1-Dioxo-1,4-dihydro-1lambda(6)-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-one analogs were discovered as a novel class of inhibitors of HCV NS5B polymerase. Structure-based design led to the identification of compound 3a that displayed potent inhibitory activities in biochemical and replicon assays (1b IC(50)<10 nM; 1b EC(50)=1.1 nM) as well as good stability toward human liver microsomes (HLM t(1/2)>60 min).

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-DIRECTED RNA POLYMERASEA, B578N/AMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
321
Query on 321
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-{3-[5-hydroxy-2-(3-methylbutyl)-3-oxo-6-thiophen-2-yl-2,3-dihydropyridazin-4-yl]-1,1-dioxido-2H-1,4-benzothiazin-7-yl}methanesulfonamide
C22 H24 N4 O6 S3
KLPXSYJOJCQFSY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
321 BindingDB:  3CWJ IC50: 10 (nM) from 1 assay(s)
EC50: min: 1.1, max: 11 (nM) from 2 assay(s)
PDBBind:  3CWJ IC50: 10 (nM) from 1 assay(s)
Binding MOAD:  3CWJ IC50: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.107α = 90
b = 106.393β = 90
c = 126.731γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
EPMRphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance