8OMI

Crystal structure of the inositol hexakisphosphate kinase EhIP6KA M85 variant in complex with ATP and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor.

Aguirre, T.Dornan, G.L.Hostachy, S.Neuenschwander, M.Seyffarth, C.Haucke, V.Schutz, A.von Kries, J.P.Fiedler, D.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.88982
  • Primary Citation of Related Structures:  
    8OMI

  • PubMed Abstract: 

    Inositol hexakisphosphate kinases (IP6Ks) are emerging as relevant pharmacological targets because a multitude of disease-related phenotypes has been associated with their function. While the development of potent IP6K inhibitors is gaining momentum, a pharmacological tool to distinguish the mammalian isozymes is still lacking. Here, we implemented an analog-sensitive approach for IP6Ks and performed a high-throughput screen to identify suitable lead compounds. The most promising hit, FMP-201300, exhibited high potency and selectivity toward the unique valine gatekeeper mutants of IP6K1 and IP6K2, compared to the respective wild-type (WT) kinases. Biochemical validation experiments revealed an allosteric mechanism of action that was corroborated by hydrogen deuterium exchange mass spectrometry measurements. The latter analysis suggested that displacement of the α C helix, caused by the gatekeeper mutation, facilitates the binding of FMP-201300 to an allosteric pocket adjacent to the ATP-binding site. FMP-201300 therefore serves as a valuable springboard for the further development of compounds that can selectively target the three mammalian IP6Ks; either as analog-sensitive kinase inhibitors or as an allosteric lead compound for the WT kinases.


  • Organizational Affiliation

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinase248Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI7A_103520
EC: 2.7
UniProt
Find proteins for N9UNA8 (Entamoeba histolytica HM-1:IMSS-A)
Explore N9UNA8 
Go to UniProtKB:  N9UNA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN9UNA8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.82α = 90
b = 102.82β = 90
c = 111.61γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermany--
German Research Foundation (DFG)GermanyEXC 2008-390540038

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-10
    Type: Initial release