4YD0

Influenza polymerase basic protein 2 (PB2) bound to an azaindole-tetrazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Isosteric replacements of the carboxylic acid of drug candidate VX-787: Effect of charge on antiviral potency and kinase activity of azaindole-based influenza PB2 inhibitors.

Boyd, M.J.Bandarage, U.K.Bennett, H.Byrn, R.R.Davies, I.Gu, W.Jacobs, M.Ledeboer, M.W.Ledford, B.Leeman, J.R.Perola, E.Wang, T.Bennani, Y.Clark, M.P.Charifson, P.S.

(2015) Bioorg.Med.Chem.Lett. 25: 1990-1994

  • DOI: 10.1016/j.bmcl.2015.03.013

  • PubMed Abstract: 
  • VX-787 is a first in class, orally bioavailable compound that offers unparalleled potential for the treatment of pandemic and seasonal influenza. As a part of our routine SAR exploration, carboxylic acid isosteres of VX-787 were prepared and tested a ...

    VX-787 is a first in class, orally bioavailable compound that offers unparalleled potential for the treatment of pandemic and seasonal influenza. As a part of our routine SAR exploration, carboxylic acid isosteres of VX-787 were prepared and tested against influenza A. It was found that the negative charge is important for maintaining potency and selectivity relative to kinase targets. Neutral carboxylic acid replacements generally resulted in compounds that were significantly less potent and less selective relative to the charged species.


    Organizational Affiliation

    Vertex Pharmaceuticals Inc., 50 Northern Avenue, Boston, MA, USA. Electronic address: Michael_Boyd@vrtx.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase basic protein 2
A
169Influenza A virus (strain A/Beijing/39/1975 H3N2)Mutation(s): 0 
Gene Names: PB2
Find proteins for Q30NP1 (Influenza A virus (strain A/Beijing/39/1975 H3N2))
Go to UniProtKB:  Q30NP1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4EW
Query on 4EW

Download SDF File 
Download CCD File 
A
2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoro-N-[(1R,2S,3S,4R)-3-(1H-tetrazol-5-yl)bicyclo[2.2.2]oct-2-yl]pyrimidin-4-amine
C20 H19 Cl F N9
PBMXGNXNEBOBGM-UIHHKEIPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.162 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 80.789α = 90.00
b = 80.789β = 90.00
c = 54.256γ = 120.00
Software Package:
Software NamePurpose
PROCESSdata scaling
PROCESSdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-02-20 
  • Released Date: 2015-04-15 
  • Deposition Author(s): Jacobs, M.D.

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references