6E3M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 

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
  • Primary Citation of Related Structures:  
    6E4C, 6E3M, 6E3O, 6E3N, 6E3P, 6E6X, 6E6W, 6E6V

  • 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 pharmacophores (MBPs) for PA N endonuclease inhibition, a fragment-based drug development campaign was pursued ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA192Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HOG
Query on HOG

Download Ideal Coordinates CCD File 
E [auth A]6-(3-carboxyphenyl)-3-hydroxy-4-oxo-1,4-dihydropyridine-2-carboxylic acid
C13 H9 N O6
CHARUKBQSGEOIG-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.198 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.459α = 90
b = 75.459β = 90
c = 120.567γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata 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  (Full details and data files)

  • 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