4P1U

Influenza A (flu) virus polymerase basic protein 2 (PB2) bound to VX787, an azaindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Novel, First-in-Class, Orally Bioavailable Azaindole Inhibitor (VX-787) of Influenza PB2.

Clark, M.P.Ledeboer, M.W.Davies, I.Byrn, R.A.Jones, S.M.Perola, E.Tsai, A.Jacobs, M.Nti-Addae, K.Bandarage, U.K.Boyd, M.J.Bethiel, R.S.Court, J.J.Deng, H.Duffy, J.P.Dorsch, W.A.Farmer, L.J.Gao, H.Gu, W.Jackson, K.Jacobs, D.H.Kennedy, J.M.Ledford, B.Liang, J.Maltais, F.Murcko, M.Wang, T.Wannamaker, M.W.Bennett, H.B.Leeman, J.R.McNeil, C.Taylor, W.P.Memmott, C.Jiang, M.Rijnbrand, R.Bral, C.Germann, U.Nezami, A.Zhang, Y.Salituro, F.G.Bennani, Y.L.Charifson, P.S.

(2014) J.Med.Chem. 57: 6668-6678

  • DOI: 10.1021/jm5007275
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In our effort to develop agents for the treatment of influenza, a phenotypic screening approach utilizing a cell protection assay identified a series of azaindole based inhibitors of the cap-snatching function of the PB2 subunit of the influenza A vi ...

    In our effort to develop agents for the treatment of influenza, a phenotypic screening approach utilizing a cell protection assay identified a series of azaindole based inhibitors of the cap-snatching function of the PB2 subunit of the influenza A viral polymerase complex. Using a bDNA viral replication assay (Wagaman, P. C., Leong, M. A., and Simmen, K. A. Development of a novel influenza A antiviral assay. J. Virol. Methods 2002, 105, 105-114) in cells as a direct measure of antiviral activity, we discovered a set of cyclohexyl carboxylic acid analogues, highlighted by VX-787 (2). Compound 2 shows strong potency versus multiple influenza A strains, including pandemic 2009 H1N1 and avian H5N1 flu strains, and shows an efficacy profile in a mouse influenza model even when treatment was administered 48 h after infection. Compound 2 represents a first-in-class, orally bioavailable, novel compound that offers potential for the treatment of both pandemic and seasonal influenza and has a distinct advantage over the current standard of care treatments including potency, efficacy, and extended treatment window.


    Organizational Affiliation

    Vertex Pharmaceuticals Inc. , 50 Northern Ave, Boston, Massachusetts 02210, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
A
169Influenza A virus (strain A/Victoria/3/1975 H3N2)Mutation(s): 0 
Gene Names: PB2
Find proteins for P31345 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Go to UniProtKB:  P31345
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
21G
Query on 21G

Download SDF File 
Download CCD File 
A
(2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid
C20 H19 F2 N5 O2
JGPXDNKSIXAZEQ-UIHHKEIPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.178 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 81.174α = 90.00
b = 81.174β = 90.00
c = 54.427γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BUSTERrefinement
REFMACrefinement
XSCALEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-27 
  • Released Date: 2014-07-30 
  • Deposition Author(s): Jacobs, M.D.

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references