8OMI | pdb_00008omi

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 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8OMI

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 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.

Macromolecule Content 

  • Total Structure Weight: 30.07 kDa 
  • Atom Count: 2,233 
  • Modeled Residue Count: 240 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinase248Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI7A_103520
EC: 2.7
UniProt
Find proteins for C4M387 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
Explore C4M387 
Go to UniProtKB:  C4M387
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4M387
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
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

View Full Validation Report



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