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 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acsmedchemlett.6b00486
  • Primary Citation of Related Structures:  
    5JUN, 5JUR

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
Molecule Chains  Sequence Length Organism Details Image
Polymerase basic protein 2
A
169 Influenza A virus (A/Beijing/39/1975(H3N2)) Mutation(s): 1 
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 Clusters 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group Q30NP1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
ID Chains  Name / Formula / InChI Key 2D Diagram 3D Interactions
6NU
Query on 6NU
Download Ideal Coordinates CCD File 
 B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 65
Unit Cell:
Length ( Å ) Angle ( ˚ )
a = 81.36 α = 90
b = 81.36 β = 90
c = 54.82 γ = 120
Software Package:
Software Name Purpose
SCALA data scaling
BUSTER-TNT refinement
PDB_EXTRACT data extraction
XDS data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description