6YM3

Crystal structure of Compound 1 with PIP4K2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A.

Wortmann, L.Brauer, N.Holton, S.J.Irlbacher, H.Weiske, J.Lechner, C.Meier, R.Karen, J.Sioberg, C.B.Putter, V.Christ, C.D.Ter Laak, A.Lienau, P.Lesche, R.Nicke, B.Cheung, S.H.Bauser, M.Haegebarth, A.von Nussbaum, F.Mumberg, D.Lemos, C.

(2021) J Med Chem 64: 15883-15911

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01245
  • Primary Citation of Related Structures:  
    6YM3, 6YM4, 6YM5

  • PubMed Abstract: 

    PIP4K2A is an insufficiently studied type II lipid kinase that catalyzes the conversion of phosphatidylinositol-5-phosphate (PI5P) into phosphatidylinositol 4,5-bisphosphate (PI4,5P 2 ). The involvement of PIP4K2A/B in cancer has been suggested, particularly in the context of p53 mutant/null tumors. PIP4K2A/B depletion has been shown to induce tumor growth inhibition, possibly due to hyperactivation of AKT and reactive oxygen species-mediated apoptosis. Herein, we report the identification of the novel potent and highly selective inhibitors BAY-091 and BAY-297 of the kinase PIP4K2A by high-throughput screening and subsequent structure-based optimization. Cellular target engagement of BAY-091 and BAY-297 was demonstrated using cellular thermal shift assay technology. However, inhibition of PIP4K2A with BAY-091 or BAY-297 did not translate into the hypothesized mode of action and antiproliferative activity in p53-deficient tumor cells. Therefore, BAY-091 and BAY-297 serve as valuable chemical probes to study PIP4K2A signaling and its involvement in pathophysiological conditions such as cancer.


  • Organizational Affiliation

    Bayer AG, Research & Development, Pharmaceuticals, 13353 Berlin, Germany.


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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHD
Query on PHD
A, B
L-PEPTIDE LINKINGC4 H8 N O7 PASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.934α = 90
b = 98.132β = 92.96
c = 104.256γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-24
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description