9U4S | pdb_00009u4s

Crystal Structure of PI5P4K-gamma in complex with n40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.304 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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Literature

Orthosteric-allosteric dual inhibitors of PI5P4K gamma with potent antitumor activity in non-small cell lung cancer.

Xiong, L.Tang, L.Zhao, W.Wang, R.Cheng, C.Wang, D.Xu, Y.Tang, L.Fan, Y.

(2025) J Adv Res 

  • DOI: https://doi.org/10.1016/j.jare.2025.09.024
  • Primary Citation of Related Structures:  
    9U4S

  • PubMed Abstract: 

    Phosphatidylinositol 5-phosphate 4-kinase type II gamma (PI5P4Kγ) has emerged as a promising therapeutic target in oncology due to its key role in cancer progression. However, currently available inhibitors targeting either the orthosteric or allosteric sites of PI5P4Kγ suffer from limited in vitro activity and in vivo validation. This study aimed to develop a highly potent and selective PI5P4Kγ inhibitor capable of simultaneously engaging both the orthosteric and allosteric sites, as well as to validate their potential in therapy for non-small cell lung cancer (NSCLC) were investigated. Through the structural modification of the propionamide side chain of the pyridine ring and the N3 substituent of the quinazolinone, the structure-activity relationship (SAR) was elucidated, leading to the identification of the target compound n40. The binding mode of n40 to PI5P4Kγ, was elucidated by X-ray crystallography. In vitro effects were assessed through KINOMEscan Technology, cell proliferation, apoptosis, and EMT analysis. In vivo efficacy was evaluated using an HCC827 xenograft mouse model. Both single-dose (up to 400 mg/kg) and repeated-dose (20-180 mg/kg/day for 28 days) toxicity studies of n40 were conducted in mice, with comprehensive monitoring of physiological parameters and organ toxicity indices. Compound n40 exhibited a strong binding affinity for PI5P4Kγ (K d  = 6.55 nM), with 3,000-fold selectivity over other two isoforms. Additionally, it displayed sub-50 nM antiproliferative activity in NSCLC cells with higher PI5P4Kγ levels. X-ray crystallography revealed n40 simultaneously binds to both orthosteric and a novelallosteric pocket. Functionally, n40 induced S-phase arrest, apoptosis, and EMT reversal and PI3K/AKT/mTOR signaling inhibition in a PI5P4Kγ-dependent manner. In HCC827 xenografts, n40 achieved > 60 % tumor growth inhibition without any observed toxicity. This study establishes PI5P4Kγ as a druggable target in NSCLC and demonstrates that dual orthosteric-allosteric targeting is a viable strategy to achieve potent and selective PI5P4Kγ inhibitors.


  • Organizational Affiliation
    • State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, School of Pharmaceutical Sciences, Guizhou Medical University, Natural Products Research Center of Guizhou Province, Guiyang 550014, China.

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
349Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.304 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 263.91α = 90
b = 47.76β = 90
c = 66.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release