6OSP

Crystal Structure Analysis of PIP4K2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors.

Sivakumaren, S.C.Shim, H.Zhang, T.Ferguson, F.M.Lundquist, M.R.Browne, C.M.Seo, H.S.Paddock, M.N.Manz, T.D.Jiang, B.Hao, M.F.Krishnan, P.Wang, D.G.Yang, T.J.Kwiatkowski, N.P.Ficarro, S.B.Cunningham, J.M.Marto, J.A.Dhe-Paganon, S.Cantley, L.C.Gray, N.S.

(2020) Cell Chem Biol 27: 525

  • DOI: https://doi.org/10.1016/j.chembiol.2020.02.003
  • Primary Citation of Related Structures:  
    6OSP

  • PubMed Abstract: 

    The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here, we present the discovery and characterization of a pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K's reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.


  • Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
A, B
394Homo sapiensMutation(s): 0 
Gene Names: PIP4K2APIP5K2PIP5K2A
EC: 2.7.1.149
UniProt & NIH Common Fund Data Resources
Find proteins for P48426 (Homo sapiens)
Explore P48426 
Go to UniProtKB:  P48426
PHAROS:  P48426
GTEx:  ENSG00000150867 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48426
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
N51 Binding MOAD:  6OSP IC50: 190 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.19α = 90
b = 98.68β = 93.66
c = 105.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description