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 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2015.03.013
  • Primary Citation of Related Structures:  
    4YD0

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2169Influenza A virus (A/Beijing/39/1975(H3N2))Mutation(s): 0 
Gene Names: PB2
UniProt
Find proteins for Q30NP1 (Influenza A virus (strain A/Beijing/39/1975 H3N2))
Explore Q30NP1 
Go to UniProtKB:  Q30NP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ30NP1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4EW
Query on 4EW

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.789α = 90
b = 80.789β = 90
c = 54.256γ = 120
Software Package:
Software NamePurpose
PROCESSdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PROCESSdata reduction
BUSTER-TNTphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary