3UDL

3-heterocyclyl quinolone bound to HCV NS5B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Quinolones as HCV NS5B polymerase inhibitors.

Kumar, D.V.Rai, R.Brameld, K.A.Somoza, J.R.Rajagopalan, R.Janc, J.W.Xia, Y.M.Ton, T.L.Shaghafi, M.B.Hu, H.Lehoux, I.To, N.Young, W.B.Green, M.J.

(2011) Bioorg Med Chem Lett 21: 82-87

  • DOI: 10.1016/j.bmcl.2010.11.068
  • Primary Citation of Related Structures:  
    3PHE, 3UDL

  • PubMed Abstract: 
  • Hepatitis C virus (HCV) infection is treated with a combination of peginterferon alfa-2a/b and ribavirin. To address the limitations of this therapy, numerous small molecule agents are in development, which act by directly affecting key steps in the viral life-cycle ...

    Hepatitis C virus (HCV) infection is treated with a combination of peginterferon alfa-2a/b and ribavirin. To address the limitations of this therapy, numerous small molecule agents are in development, which act by directly affecting key steps in the viral life-cycle. Herein we describe our discovery of quinolone derivatives, novel small-molecules that inhibit NS5b polymerase, a key enzyme of the viral life-cycle. A crystal structure of a quinoline analog bound to NS5B reveals that this class of compounds binds to allosteric site-II (non-nucleoside inhibitor-site 2, NNI-2) of this protein.


    Organizational Affiliation

    Myriad Pharmaceuticals, 305 Chipeta Way, Salt Lake City, UT 84108, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS5B polymeraseA, B, C, D576Hepatitis C virus subtype 1bMutation(s): 0 
EC: 3.4.22 (UniProt), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Explore P26663 
Go to UniProtKB:  P26663
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KLI (Subject of Investigation/LOI)
Query on KLI

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]3-(5-benzyl-1,2,4-oxadiazol-3-yl)-6-fluoro-1-[2-fluoro-4-(trifluoromethyl)benzyl]-7-(4-methylpiperazin-1-yl)quinolin-4(1H)-one
C31 H26 F5 N5 O2
BZDUJTPAUCQOHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.746α = 90
b = 101.863β = 90
c = 250.867γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
BOSdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2011-10-28 
  • Released Date: 2011-12-21 
  • Deposition Author(s): Somoza, J.R.

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release