5WB3

Crystal structure of the influenza virus PA endonuclease in complex with inhibitor 10j (SRI-30026)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    5W3I, 5W44, 5W73, 5W7U, 5W92, 5W9G, 5WA6, 5WA7, 5WAP, 5WB3, 5WCS, 5WCT, 5WDC, 5WDN, 5WDW, 5WE9, 5WEB, 5WEF, 5WEI, 5WF3, 5WFM, 5WFW, 5WFZ, 5WG9

  • 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 constantly evolving nature of this virus ...

    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. thomas.webb@sri.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polymerase acidic proteinA197Influenza 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GYA (Subject of Investigation/LOI)
Query on GYA

Download Ideal Coordinates CCD File 
F [auth A]2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(5,6-dimethoxy-2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-ox o-1,6-dihydropyrimidine-4-carboxamide
C28 H29 Cl N4 O6 S
DUURZOUMZXZFQN-IBGZPJMESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
Binding Affinity Annotations 
IDSourceBinding Affinity
GYA Binding MOAD:  5WB3 Ki: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.698α = 90
b = 90.698β = 90
c = 134.31γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

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--
St. Jude Children's Research Hospital (ALSAC)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Structure summary
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence