6NEM | pdb_00006nem

3-hydroxy-5-[(naphthalen-1-yl)methyl]-6-[4-(1H-tetrazol-5-yl)phenyl]pyridin-2(1H)-one bound to influenza 2009 pH1N1 endonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.203 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Aryl and Arylalkyl Substituted 3-Hydroxypyridin-2(1H)-ones: Synthesis and Evaluation as Inhibitors of Influenza A Endonuclease.

Sagong, H.Y.Bauman, J.D.Nogales, A.Martinez-Sobrido, L.Arnold, E.LaVoie, E.J.

(2019) ChemMedChem 14: 1204-1223

  • DOI: https://doi.org/10.1002/cmdc.201900084
  • Primary Citation Related Structures: 
    6NEL, 6NEM

  • PubMed Abstract: 

    Seasonal influenza infections are associated with an estimated 250-500 000 deaths annually. Resistance to the antiviral M2 ion-channel inhibitors has largely invalidated their clinical utility. Resistance to neuraminidase inhibitors has also been observed in several influenza A virus (IAV) strains. These data have prompted research on inhibitors that target the cap-snatching endonuclease activity of the polymerase acidic protein (PA). Baloxavir marboxil (Xofluza®), recently approved for clinical use, inhibits cap-snatching endonuclease. Resistance to Xofluza® has been reported in both in vitro systems and in the clinic. An X-ray crystallographic screening campaign of a fragment library targeting IAV endonuclease identified 5-chloro-3-hydroxypyridin-2(1H)-one as a bimetal chelating agent at the active site. We have reported the structure-activity relationships for 3-hydroxypyridin-2(1H)-ones and 3-hydroxyquinolin-2(1H)-ones as endonuclease inhibitors. These studies identified two distinct binding modes associated with inhibition of this enzyme that are influenced by the presence of substituents at the 5- and 6-positions of 3-hydroxypyridin-2(1H)-ones. Herein we report the structure-activity relationships associated with various para-substituted 5-phenyl derivatives of 6-(p-fluorophenyl)-3-hydroxypyridin-2(1H)-ones and the effect of using naphthyl, benzyl, and naphthylmethyl groups as alternatives to the p-fluorophenyl substituent on their activity as endonuclease inhibitors.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA.

Macromolecule Content 

  • Total Structure Weight: 29.16 kDa 
  • Atom Count: 1,819 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 241 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polymerase acidic protein241Influenza A virus (A/Luxembourg/43/2009(H1N1))Mutation(s): 0 
Gene Names: PA
UniProt
Find proteins for C6H0Y9 (Influenza A virus)
Explore C6H0Y9 
Go to UniProtKB:  C6H0Y9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6H0Y9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.203 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.505α = 90
b = 100.996β = 90
c = 66.204γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesAI119321

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description