8DPJ

The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023030


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.

Slavish, P.J.Cuypers, M.G.Rimmer, M.A.Abdolvahabi, A.Jeevan, T.Kumar, G.Jarusiewicz, J.A.Vaithiyalingam, S.Jones, J.C.Bowling, J.J.Price, J.E.DuBois, R.M.Min, J.Webby, R.J.Rankovic, Z.White, S.W.

(2023) Eur J Med Chem 247: 115035-115035

  • DOI: https://doi.org/10.1016/j.ejmech.2022.115035
  • Primary Citation of Related Structures:  
    6V6X, 6V9E, 6VBR, 6VG9, 6VIV, 6VJH, 6VL3, 6WIJ, 6WJ4, 7K87, 7LM4, 7LW6, 7M0N, 7MPF, 7MTY, 7N47, 7N55, 7N68, 7N8F, 7RKP, 7UMR, 7UUH, 8DIP, 8DPJ, 8DTW, 8E4S

  • PubMed Abstract: 

    Influenza is one of the leading causes of disease-related mortalities worldwide. Several strategies have been implemented during the past decades to hinder the replication cycle of influenza viruses, all of which have resulted in the emergence of resistant virus strains. The most recent example is baloxavir marboxil, where a single mutation in the active site of the target endonuclease domain of the RNA-dependent-RNA polymerase renders the recent FDA approved compound ∼1000-fold less effective. Raltegravir is a first-in-class HIV inhibitor that shows modest activity to the endonuclease. Here, we have used structure-guided approaches to create rationally designed derivative molecules that efficiently engage the endonuclease active site. The design strategy was driven by our previously published structures of endonuclease-substrate complexes, which allowed us to target functionally conserved residues and reduce the likelihood of resistance mutations. We succeeded in developing low nanomolar equipotent inhibitors of both wild-type and baloxavir-resistant endonuclease. We also developed macrocyclic versions of these inhibitors that engage the active site in the same manner as their 'open' counterparts but with reduced affinity. Structural analyses provide clear avenues for how to increase the affinity of these cyclic compounds.


  • Organizational Affiliation

    Departments of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein PA-X197Influenza A virusMutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QQ4
Query on QQ4

Download Ideal Coordinates CCD File 
D [auth A]Hexa Vinylpyrrolidone K15
C36 H56 N6 O6
OFPQNVWJHZVWCZ-CMPUJJQDSA-N
SE9 (Subject of Investigation/LOI)
Query on SE9

Download Ideal Coordinates CCD File 
E [auth A](2P)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide
C20 H17 F3 N4 O4
CJUKCSPPUSTPJP-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.598α = 90
b = 89.598β = 90
c = 134.158γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-03-29
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description