5WFZ

Crystal structure of the influenza virus PA endonuclease (E119D mutant) in complex with inhibitor 8e (SRI-30049)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease.

Beylkin, D.Kumar, G.Zhou, W.Park, J.Jeevan, T.Lagisetti, C.Harfoot, R.Webby, R.J.White, S.W.Webb, T.R.

(2017) Sci Rep 7: 17139-17139

  • DOI: 10.1038/s41598-017-17419-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Influenza is a serious hazard to human health that causes hundreds of thousands of deaths annually. Though vaccines and current therapeutics can blunt some of the perilous impact of this viral infection, new treatments are needed due to the constantl ...

    Influenza is a serious hazard to human health that causes hundreds of thousands of deaths annually. Though vaccines and current therapeutics can blunt some of the perilous impact of this viral infection, new treatments are needed due to the constantly evolving nature of this virus. Recently, our growing understanding of an essential influenza viral protein, PA, has led to the development of focused libraries of new small molecules that specifically target the active site of the PA influenza endonuclease, which we report here. Our overarching approach has been to proactively develop lead inhibitors that are less likely to rapidly develop clinical resistance by optimizing inhibitors that retain activity against induced resistant mutants. Here, we report details behind the discovery of new potent inhibitors of wild type and resistant mutant endonucleases along with their high-resolution co-crystal structure-activity relationships. These results add to our understanding of nuclease protein targets and potentially serve as starting points for a new therapeutic approach to the treatment of influenza.


    Organizational Affiliation

    Bioscience Division, SRI International, Menlo Park, CA, 94025, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polymerase acidic protein
A
197Influenza A virus (strain swl A/California/04/2009 H1N1)Mutation(s): 1 
Gene Names: PA
EC: 3.1.-.-
Find proteins for C3W5S0 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Go to UniProtKB:  C3W5S0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
KU0
Query on KU0

Download SDF File 
Download CCD File 
A
2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-[2-(phenylsulfonyl)ethyl]-1,6-dihydropyrimidine-4-carboxamide
C23 H21 Cl2 N5 O6 S
YFLBJSGKKSRTGS-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.207 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.300α = 90.00
b = 90.300β = 90.00
c = 133.353γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-13 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Kumar, G., White, S.W.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI098757
St. Jude Children's Research HospitalUnited States--
ALSACUnited States--

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release