4YD0 | pdb_00004yd0

Influenza polymerase basic protein 2 (PB2) bound to an azaindole-tetrazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4YD0/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Influenza A virus (A/Beijing/39/1975(H3N2))
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-20 Released: 2015-04-15 
• Deposition Author(s): Jacobs, M.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.216 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Isosteric replacements of the carboxylic acid of drug candidate VX-787: Effect of charge on antiviral potency and kinase activity of azaindole-based influenza PB2 inhibitors.

Boyd, M.J., Bandarage, U.K., Bennett, H., Byrn, R.R., Davies, I., Gu, W., Jacobs, M., Ledeboer, M.W., Ledford, B., Leeman, J.R., Perola, E., Wang, T., Bennani, Y., Clark, M.P., Charifson, P.S.

(2015) Bioorg Med Chem Lett 25: 1990-1994

• PubMed: 25827523 
• DOI: https://doi.org/10.1016/j.bmcl.2015.03.013
• Primary Citation Related Structures: 
  4YD0


• PubMed Abstract: 
  

  VX-787 is a first in class, orally bioavailable compound that offers unparalleled potential for the treatment of pandemic and seasonal influenza. As a part of our routine SAR exploration, carboxylic acid isosteres of VX-787 were prepared and tested against influenza A. It was found that the negative charge is important for maintaining potency and selectivity relative to kinase targets. Neutral carboxylic acid replacements generally resulted in compounds that were significantly less potent and less selective relative to the charged species.

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Organizational Affiliation: 
• Vertex Pharmaceuticals Inc., 50 Northern Avenue, Boston, MA, USA. Electronic address: [e-mail].
Vertex Pharmaceuticals Inc., 50 Northern Avenue, Boston, MA, USA.

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: 19.61 kDa 
• Atom Count: 1,366 
• Modeled Residue Count: 161 
• 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): 0  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
4EW	B [auth A]	2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoro-N-[(1R,2S,3S,4R)-3-(1H-tetrazol-5-yl)bicyclo[2.2.2]oct-2-yl]pyrimidin-4-amine C20 H19 Cl F N9 PBMXGNXNEBOBGM-UIHHKEIPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.216 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.789	α = 90
b = 80.789	β = 90
c = 54.256	γ = 120

Software Package:

Software Name	Purpose
PROCESS	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
PROCESS	data reduction
BUSTER-TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Jacobs, M.D.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2015-05-06
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary