5JUN

PB2 bound to an azaindole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Novel, Orally Bioavailable beta-Amino Acid Azaindole Inhibitors of Influenza PB2.

Farmer, L.J.Clark, M.P.Boyd, M.J.Perola, E.Jones, S.M.Tsai, A.Jacobs, M.D.Bandarage, U.K.Ledeboer, M.W.Wang, T.Deng, H.Ledford, B.Gu, W.Duffy, J.P.Bethiel, R.S.Shannon, D.Byrn, R.A.Leeman, J.R.Rijnbrand, R.Bennett, H.B.O'Brien, C.Memmott, C.Nti-Addae, K.Bennani, Y.L.Charifson, P.S.

(2017) ACS Med Chem Lett 8: 256-260

  • DOI: 10.1021/acsmedchemlett.6b00486
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In our efforts to develop novel small-molecule inhibitors for the treatment of influenza, we utilized molecular modeling and the X-ray crystal structure of the PB2 subunit of the influenza polymerase to optimize a series of acyclic β-amino acid inhib ...

    In our efforts to develop novel small-molecule inhibitors for the treatment of influenza, we utilized molecular modeling and the X-ray crystal structure of the PB2 subunit of the influenza polymerase to optimize a series of acyclic β-amino acid inhibitors, highlighted by compound 4. Compound 4 showed good oral exposure in both rat and mouse. More importantly, it showed strong potency versus multiple influenza-A strains, including pandemic 2009 H1N1 and avian H5N1 strains and showed a strong efficacy profile in a mouse influenza model even when treatment was initiated 48 h after infection. Compound 4 offers good oral bioavailability with great potential for the treatment of both pandemic and seasonal influenza.


    Organizational Affiliation

    Vertex Pharmaceuticals Inc. , 50 Northern Avenue, 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/Beijing/39/1975 H3N2)Mutation(s): 1 
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
6NU
Query on 6NU

Download SDF File 
Download CCD File 
A
(3~{R})-3-[[5-fluoranyl-2-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]-3-(1-methylcyclobutyl)propanoic acid
C19 H19 F2 N5 O2
BEVIQKVDXVXDJA-CQSZACIVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.176 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 81.360α = 90.00
b = 81.360β = 90.00
c = 54.820γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-05-10 
  • Released Date: 2017-05-17 
  • Deposition Author(s): Jacobs, M.D.

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description