5BUH

Influenza PB2 bound to a hydroxymethyl azaindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel 2-Substituted 7-Azaindole and 7-Azaindazole Analogues as Potential Antiviral Agents for the Treatment of Influenza.

Bandarage, U.K.Clark, M.P.Perola, E.Gao, H.Jacobs, M.D.Tsai, A.Gillespie, J.Kennedy, J.M.Maltais, F.Ledeboer, M.W.Davies, I.Gu, W.Byrn, R.A.Nti Addae, K.Bennett, H.Leeman, J.R.Jones, S.M.O'Brien, C.Memmott, C.Bennani, Y.Charifson, P.S.

(2017) ACS Med Chem Lett 8: 261-265

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00487
  • Primary Citation of Related Structures:  
    5BUH, 5F79

  • PubMed Abstract: 

    JNJ-63623872 ( 2 ) is a first-in-class, orally bioavailable compound that offers significant potential for the treatment of pandemic and seasonal influenza. Early lead optimization efforts in our 7-azaindole series focused on 1,3-diaminocyclohexyl amide and urea substitutions on the pyrimidine-7-azaindole motif. In this work, we explored two strategies to eliminate observed aldehyde oxidase (AO)-mediated metabolism at the 2-position of these 7-azaindole analogues. Substitution at the 2-position of the azaindole ring generated somewhat less potent analogues, but reduced AO-mediated metabolism. Incorporation of a ring nitrogen generated 7-azaindazole analogues that were equipotent to the parent 2-H-7-azaindole, but surprisingly, did not appear to improve AO-mediated metabolism. Overall, we identified multiple 2-substituted 7-azaindole analogues with enhanced AO stability and we present data for one such compound ( 12 ) that demonstrate a favorable oral pharmacokinetic profile in rodents. These analogues have the potential to be further developed as anti-influenza agents for the treatment of influenza.


  • Organizational Affiliation

    Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, 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/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
4V7
Query on 4V7

Download Ideal Coordinates CCD File 
B [auth A]N-[(1R,3S)-3-({5-fluoro-2-[5-fluoro-2-(hydroxymethyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]pyrimidin-4-yl}amino)cyclohexyl]pyrrolidine-1-carboxamide
C23 H27 F2 N7 O2
GNSZLKHAOIWBEM-LSDHHAIUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.801α = 90
b = 81.801β = 90
c = 55.598γ = 120
Software Package:
Software NamePurpose
autoPROCdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-06-08 
  • Deposition Author(s): Jacobs, M.D.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description