2HAI

Crystal structure of HCV NS5B RNA polymerase in complex with novel class of dihydropyrone-containing inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and structure-based optimization of novel dihydropyrones as potent HCV RNA polymerase inhibitors.

Li, H.Tatlock, J.Linton, A.Gonzalez, J.Borchardt, A.Dragovich, P.Jewell, T.Prins, T.Zhou, R.Blazel, J.Parge, H.Love, R.Hickey, M.Doan, C.Shi, S.Duggal, R.Lewis, C.Fuhrman, S.

(2006) Bioorg.Med.Chem.Lett. 16: 4834-4838

  • DOI: 10.1016/j.bmcl.2006.06.065

  • PubMed Abstract: 
  • A novel class of non-nucleoside HCV NS5B polymerase inhibitors has been identified from screening. A co-crystal structure revealed an allosteric binding site in the protein that required a unique conformational change to accommodate inhibitor binding ...

    A novel class of non-nucleoside HCV NS5B polymerase inhibitors has been identified from screening. A co-crystal structure revealed an allosteric binding site in the protein that required a unique conformational change to accommodate inhibitor binding. Herein we report the structure-activity relationships (SARs) of this novel class of dihydropyrone-containing compounds that show potent inhibitory activities against the HCV RNA polymerase in biochemical assays.


    Organizational Affiliation

    Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Dr., San Diego, CA 92121, USA. hui.li@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEPATITIS C VIRUS NS5B RNA POLYMERASE
A
576Hepatitis C virus subtype 1bMutation(s): 3 
Find proteins for Q99AU2 (Hepatitis C virus subtype 1b)
Go to UniProtKB:  Q99AU2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PFI
Query on PFI

Download SDF File 
Download CCD File 
A
(6S)-6-CYCLOPENTYL-6-[2-(3-FLUORO-4-ISOPROPOXYPHENYL)ETHYL]-4-HYDROXY-5,6-DIHYDRO-2H-PYRAN-2-ONE
C21 H27 F O4
AKNIHFDXRAOPAI-NRFANRHFSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFIIC50: 530 nM BINDINGMOAD
PFIIC50: 530 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.255α = 90.00
b = 83.255β = 90.00
c = 179.830γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-12 
  • Released Date: 2006-09-05 
  • Deposition Author(s): Li, H., Love, R.L.

Revision History 

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance