7Z75

PI3KC2a core in complex with PITCOIN3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development of selective inhibitors of phosphatidylinositol 3-kinase C2 alpha.

Lo, W.T.Belabed, H.Kucukdisli, M.Metag, J.Roske, Y.Prokofeva, P.Ohashi, Y.Horatscheck, A.Cirillo, D.Krauss, M.Schmied, C.Neuenschwander, M.von Kries, J.P.Medard, G.Kuster, B.Perisic, O.Williams, R.L.Daumke, O.Payrastre, B.Severin, S.Nazare, M.Haucke, V.

(2023) Nat Chem Biol 19: 18-27

  • DOI: https://doi.org/10.1038/s41589-022-01118-z
  • Primary Citation of Related Structures:  
    7Z74, 7Z75, 8A9I

  • PubMed Abstract: 

    Phosphatidylinositol 3-kinase type 2α (PI3KC2α) and related class II PI3K isoforms are of increasing biomedical interest because of their crucial roles in endocytic membrane dynamics, cell division and signaling, angiogenesis, and platelet morphology and function. Herein we report the development and characterization of PhosphatidylInositol Three-kinase Class twO INhibitors (PITCOINs), potent and highly selective small-molecule inhibitors of PI3KC2α catalytic activity. PITCOIN compounds exhibit strong selectivity toward PI3KC2α due to their unique mode of interaction with the ATP-binding site of the enzyme. We demonstrate that acute inhibition of PI3KC2α-mediated synthesis of phosphatidylinositol 3-phosphates by PITCOINs impairs endocytic membrane dynamics and membrane remodeling during platelet-dependent thrombus formation. PITCOINs are potent and selective cell-permeable inhibitors of PI3KC2α function with potential biomedical applications ranging from thrombosis to diabetes and cancer.


  • Organizational Affiliation

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha910Mus musculusMutation(s): 3 
Gene Names: Pik3c2aCpk
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.1.154 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q61194 (Mus musculus)
Explore Q61194 
Go to UniProtKB:  Q61194
IMPC:  MGI:1203729
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61194
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IG3 (Subject of Investigation/LOI)
Query on IG3

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[4-[3-(methylsulfonylamino)phenyl]-1,3-thiazol-2-yl]-2-[4-oxidanylidene-3-(2-phenylethyl)pteridin-2-yl]sulfanyl-ethanamide
C26 H23 N7 O4 S3
ZQUVBPXCXCKORU-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.064α = 90
b = 134.412β = 90
c = 152.679γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description