1YVF

Hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00729145


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid.

Pfefferkorn, J.A.Greene, M.L.Nugent, R.A.Gross, R.J.Mitchell, M.A.Finzel, B.C.Harris, M.S.Wells, P.A.Shelly, J.A.Anstadt, R.A.Kilkuskie, R.E.Kopta, L.A.Schwende, F.J.

(2005) Bioorg.Med.Chem.Lett. 15: 2481-2486

  • DOI: 10.1016/j.bmcl.2005.03.066

  • PubMed Abstract: 
  • A novel series of nonnucleoside HCV NS5B polymerase inhibitors were prepared from (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid, a high throughput screening lead. SAR studies combined with structure based drug design focusing on the southern ...

    A novel series of nonnucleoside HCV NS5B polymerase inhibitors were prepared from (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid, a high throughput screening lead. SAR studies combined with structure based drug design focusing on the southern heterobiaryl region of the template led to the synthesis of several potent and orally bioavailable lead compounds. X-ray crystallography studies were also performed to understand the interaction of these inhibitors with HCV NS5B polymerase.


    Related Citations: 
    • Inhibitors of HCV NS5B polymerase: Part 2: Evaluation of the northern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid
      Pfefferkorn, J.A.,Nugent, R.A.,Gross, R.J.,Greene, M.L.,Mitchell, M.A.,Reding, M.T.,Funk, L.A.,Anderson, R.,Wells, P.A.,Shelly, J.A.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. jeffrey.a.pfefferkorn@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HCV NS5B POLYMERASE
A
577Hepacivirus CMutation(s): 0 
Find proteins for O93077 (Hepacivirus C)
Go to UniProtKB:  O93077
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PH7
Query on PH7

Download SDF File 
Download CCD File 
A
(2Z)-2-(BENZOYLAMINO)-3-[4-(2-BROMOPHENOXY)PHENYL]-2-PROPENOIC ACID
C22 H16 Br N O4
WLPJLQNKCJWAFL-RGEXLXHISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PH7IC50: 100 nM BINDINGMOAD
PH7IC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.879α = 90.00
b = 90.879β = 90.00
c = 188.516γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description