3GYN

Crystal structure of HCV NS5B polymerase with a novel monocyclic dihydropyridinone inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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Literature

5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase.

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

(2009) Bioorg Med Chem Lett 19: 6047-6052

  • DOI: 10.1016/j.bmcl.2009.09.051
  • Primary Citation of Related Structures:  
    3GYN, 3IGV

  • PubMed Abstract: 

    • The discovery of 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of the HCV RNA-dependent RNA polymerase (NS5B) is described. Several of these agents also display potent antiviral activity in cell culture experiments (EC50 <0.10 microM) ...

    The discovery of 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of the HCV RNA-dependent RNA polymerase (NS5B) is described. Several of these agents also display potent antiviral activity in cell culture experiments (EC50 <0.10 microM). In vitro DMPK data for selected compounds as well as crystal structures of representative inhibitors complexed with the NS5B protein are also disclosed.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA, B578Hepatitis C virus (isolate BK)Mutation(s): 1 
EC: 2.7.7.48 (PDB Primary Data), 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
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
B42
Query on B42
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-{3-[(5R)-1-cyclopentyl-4-hydroxy-5-methyl-5-(3-methylbutyl)-2-oxo-1,2,5,6-tetrahydropyridin-3-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide
C24 H34 N4 O6 S2
TXEOLWVIZKSKML-XMMPIXPASA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
B42 PDBBind:  3GYN IC50: 61 (nM) from 1 assay(s)
Binding MOAD:  3GYN IC50: 47 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.864α = 90
b = 106.391β = 90
c = 126.567γ = 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: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-13
    Changes: Database references, Derived calculations