4NCE

Influenza polymerase basic protein 2 (PB2) bound to 7-methyl-GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.229 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view detailsBest fitted 11HClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1021/jm5007275
  • Primary Citation of Related Structures:  
    4NCE, 4NCM, 4P1U

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polymerase basic protein 2169Influenza A virus (A/Victoria/3/1975(H3N2))Mutation(s): 0 
Gene Names: PB2polymerase basic protein
UniProt
Find proteins for P31345 (Influenza A virus (strain A/Victoria/3/1975 H3N2))
Explore P31345 
Go to UniProtKB:  P31345
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31345
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.44α = 90
b = 81.44β = 90
c = 54.56γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view detailsBest fitted 11HClick on this verticalbar to view details

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-06
    Changes: Database references
  • Version 1.2: 2014-08-27
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description