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 5EGA | pdb_00005ega

2009 H1N1 PA endonuclease domain in complex with an N-acylhydrazone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.234 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

N-acylhydrazone inhibitors of influenza virus PA endonuclease with versatile metal binding modes.

Carcelli, M., Rogolino, D., Gatti, A., De Luca, L., Sechi, M., Kumar, G., White, S.W., Stevaert, A., Naesens, L.

(2016) Sci Rep 6: 31500-31500

  • DOI: https://doi.org/10.1038/srep31500
  • Primary Citation Related Structures: 
    5EGA

  • PubMed Abstract: 

    Influenza virus PA endonuclease has recently emerged as an attractive target for the development of novel antiviral therapeutics. This is an enzyme with divalent metal ion(s) (Mg(2+) or Mn(2+)) in its catalytic site: chelation of these metal cofactors is an attractive strategy to inhibit enzymatic activity. Here we report the activity of a series of N-acylhydrazones in an enzymatic assay with PA-Nter endonuclease, as well as in cell-based influenza vRNP reconstitution and virus yield assays. Several N-acylhydrazones were found to have promising anti-influenza activity in the low micromolar concentration range and good selectivity. Computational docking studies are carried on to investigate the key features that determine inhibition of the endonuclease enzyme by N-acylhydrazones. Moreover, we here describe the crystal structure of PA-Nter in complex with one of the most active inhibitors, revealing its interactions within the protein's active site.


  • Organizational Affiliation: 
    • Dipartimento di Chimica and Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.

Macromolecule Content 

  • Total Structure Weight: 22.4 kDa 
  • Atom Count: 1,462 
  • Modeled Residue Count: 177 
  • Deposited Residue Count: 187 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase acidic protein187Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: PA
EC: 3.1
UniProt
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S0 
Go to UniProtKB:  C3W5S0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.234 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.989α = 90
b = 73.989β = 90
c = 128.546γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI098757
St. Jude Children's Research Hospital (ALSAC)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description