3FRZ

Crystal Structure of HCV NS5B RNA polymerase in complex with PF868554


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of (R)-6-cyclopentyl-6-(2-(2,6-diethylpyridin-4-yl)ethyl)-3-((5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)methyl)-4-hydroxy-5,6-dihydropyran-2-one (PF-00868554) as a potent and orally available hepatitis C virus polymerase inhibitor.

Li, H.Tatlock, J.Linton, A.Gonzalez, J.Jewell, T.Patel, L.Ludlum, S.Drowns, M.Rahavendran, S.V.Skor, H.Hunter, R.Shi, S.T.Herlihy, K.J.Parge, H.Hickey, M.Yu, X.Chau, F.Nonomiya, J.Lewis, C.

(2009) J Med Chem 52: 1255-1258

  • DOI: 10.1021/jm8014537
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The HCV RNA-dependent RNA polymerase has emerged as one of the key targets for novel anti-HCV therapy development. Herein, we report the optimization of the dihydropyrone series inhibitors to improve compound aqueous solubility and reduce CYP2D6 inhi ...

    The HCV RNA-dependent RNA polymerase has emerged as one of the key targets for novel anti-HCV therapy development. Herein, we report the optimization of the dihydropyrone series inhibitors to improve compound aqueous solubility and reduce CYP2D6 inhibition, which led to the discovery of compound 24 (PF-00868554). Compound 24 is a potent and selective HCV polymerase inhibitor with a favorable pharmacokinetic profile and has recently entered a phase II clinical evaluation in patients with genotype 1 HCV.


    Organizational Affiliation

    Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. hui.li@pfizer.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed RNA polymerase
A
576Hepatitis C virus (isolate BK)Mutation(s): 5 
Gene Names: NS5B
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)
Find proteins for P26663 (Hepatitis C virus genotype 1b (isolate BK))
Go to UniProtKB:  P26663
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AG6
Query on AG6

Download CCD File 
A
N-[(benzyloxy)carbonyl]-L-alpha-glutamyl-N-[(1S)-4-oxo-4-phenyl-1-propylbut-2-en-1-yl]-L-phenylalaninamide
C35 H39 N3 O7
LKWUEIKYVLZLJI-DTXPUJKBSA-N
 Ligand Interaction
AG0
Query on AG0

Download CCD File 
A
(6R)-6-cyclopentyl-6-[2-(2,6-diethylpyridin-4-yl)ethyl]-3-[(5,7-dimethyl[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)methyl]-4-hydroxy-5,6-dihydro-2H-pyran-2-one
C29 H37 N5 O3
SLVAPEZTBDBAPI-GDLZYMKVSA-N
 Ligand Interaction
BME
Query on BME

Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AG0IC50:  7   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.2α = 90
b = 83.2β = 90
c = 180.263γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
ARP/wARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-01-08 
  • Released Date: 2009-03-10 
  • Deposition Author(s): Parge, H.E.

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance