8BQ4

Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Identification of Potent, Selective, and Brain Penetrant PI5P4K gamma Inhibitors as In Vivo-Ready Tool Molecules.

Rooney, T.P.C.Aldred, G.G.Boffey, H.K.Willems, H.M.G.Edwards, S.Chawner, S.J.Scott, D.E.Green, C.Winpenny, D.Skidmore, J.Clarke, J.H.Andrews, S.P.

(2023) J Med Chem 66: 804-821

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01693
  • Primary Citation of Related Structures:  
    8BQ4

  • PubMed Abstract: 

    Owing to their central role in regulating cell signaling pathways, the phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) are attractive therapeutic targets in diseases such as cancer, neurodegeneration, and immunological disorders. Until now, tool molecules for these kinases have been either limited in potency or isoform selectivity, which has hampered further investigation of biology and drug development. Herein we describe the virtual screening workflow which identified a series of thienylpyrimidines as PI5P4Kγ-selective inhibitors, as well as the medicinal chemistry optimization of this chemotype, to provide potent and selective tool molecules for further use. In vivo pharmacokinetics data are presented for exemplar tool molecules, along with an X-ray structure for ARUK2001607 ( 15 ) in complex with PI5P4Kγ, along with its selectivity data against >150 kinases and a Cerep safety panel.


  • Organizational Affiliation

    The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma
A, B
363Homo sapiensMutation(s): 0 
Gene Names: PIP4K2CPIP5K2C
EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBX8 (Homo sapiens)
Explore Q8TBX8 
Go to UniProtKB:  Q8TBX8
PHAROS:  Q8TBX8
GTEx:  ENSG00000166908 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TBX8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QZR (Subject of Investigation/LOI)
Query on QZR

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-methyl-~{N}-(4-methylsulfonylphenyl)thieno[2,3-d]pyrimidin-4-amine
C14 H13 N3 O2 S2
QVQHWPLHUNEREE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.09α = 90
b = 78.86β = 90
c = 96.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alzheimers Research UK (ARUK)United KingdomARUK-2015DDI-CAM

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description