1Z4U

hepatitis C virus NS5B RNA-dependent RNA polymerase complex with inhibitor PHA-00799585


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibitors of HCV NS5B polymerase. Part 2: Evaluation of the northern region of (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid

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

(2005) Bioorg Med Chem Lett 15: 2812-2818

  • DOI: 10.1016/j.bmcl.2005.03.106
  • Primary Citation of Related Structures:  
    1Z4U

  • PubMed Abstract: 
  • A novel series of non-nucleoside HCV NS5B polymerase inhibitors was prepared from a (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid template. Solution and solid phase analog synthesis focused on the northern region of the template combined with structure based design led to the discovery of several potent and orally bioavailable lead compounds ...

    A novel series of non-nucleoside HCV NS5B polymerase inhibitors was prepared from a (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid template. Solution and solid phase analog synthesis focused on the northern region of the template combined with structure based design led to the discovery of several potent and orally bioavailable lead compounds.


    Related Citations: 
    • 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.
      (2005) Bioorg Med Chem Lett 15: 2481

    Organizational Affiliation

    Pfizer Global Research & Development, Michigan Laboratories, Ann Arbor, 48105, USA. jeffrey.a.pfefferkorn@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HCV NS5B POLYMERASEA577Hepacivirus CMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.21.98 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt)
UniProt
Find proteins for O93077 (Hepacivirus C)
Explore O93077 
Go to UniProtKB:  O93077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93077
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PH9
Query on PH9

Download Ideal Coordinates CCD File 
D [auth A](2Z)-2-[(1-ADAMANTYLCARBONYL)AMINO]-3-[4-(2-BROMOPHENOXY)PHENYL]PROP-2-ENOIC ACID
C26 H28 Br N O4
SJHUUZUNPUEALW-ZDXWGTOVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PH9 PDBBind:  1Z4U IC50: 70 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.344α = 90
b = 91.344β = 90
c = 189.111γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description