6E3P

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 6-(3-(1H-tetrazol-5-yl)phenyl)-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease.

Credille, C.V.Morrison, C.N.Stokes, R.W.Dick, B.L.Feng, Y.Sun, J.Chen, Y.Cohen, S.M.

(2019) J Med Chem 62: 9438-9449

  • DOI: 10.1021/acs.jmedchem.9b00747
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Significant efforts have been reported on the development of influenza antivirals including inhibitors of the RNA-dependent RNA polymerase PA N-terminal (PA N ) endonuclease. Based on recently identified, highly active metal-binding pharma ...

    Significant efforts have been reported on the development of influenza antivirals including inhibitors of the RNA-dependent RNA polymerase PA N-terminal (PA N ) endonuclease. Based on recently identified, highly active metal-binding pharmacophores (MBPs) for PA N endonuclease inhibition, a fragment-based drug development campaign was pursued. Guided by coordination chemistry and structure-based drug design, MBP scaffolds were elaborated to improve activity and selectivity. Structure-activity relationships were established and used to generate inhibitors of influenza endonuclease with tight-binding affinities. The activity of these inhibitors was analyzed using a fluorescence-quenching-based nuclease activity assay, and binding was validated using differential scanning fluorometry. Lead compounds were found to be highly selective for PA N endonuclease against several related dinuclear and mononuclear metalloenzymes. Combining principles of bioinorganic and medicinal chemistry in this study has resulted in some of the most active in vitro influenza PA N endonuclease inhibitors with high ligand efficiencies.


    Organizational Affiliation

    Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic proteinA192Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: PA
EC: 3.1
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S0 
Go to UniProtKB:  C3W5S0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HO1
Query on HO1

Download CCD File 
A
3-hydroxy-4-oxo-6-[3-(1H-tetrazol-5-yl)phenyl]-1,4-dihydropyridine-2-carboxylic acid
C13 H9 N5 O4
KPXVENWWYNXYEC-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.215 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.95α = 90
b = 74.95β = 90
c = 120.759γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
APEXdata reduction
APEXdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM098435

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-29
    Changes: Database references