5JUN

PB2 bound to an azaindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5JUN/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Influenza A virus (A/Beijing/39/1975(H3N2))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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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 

Starting Model: experimental

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

• PubMed: 28197322 
• 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.

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Organizational Affiliation: 

Vertex Pharmaceuticals Inc. , 50 Northern Avenue, Boston, Massachusetts 02210, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.56 kDa 
• Atom Count: 1,302 
• Modelled Residue Count: 160 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NU	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

Entry History 

Deposition Data

• 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
  Changes: Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description