3ENE

Complex of PI3K gamma with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeted polypharmacology: discovery of dual inhibitors of tyrosine and phosphoinositide kinases

Apsel, B.Blair, J.A.Gonzalez, B.Nazif, T.M.Feldman, M.E.Aizenstein, B.Hoffman, R.Williams, R.L.Shokat, K.M.Knight, Z.A.

(2008) Nat.Chem.Biol. 4: 691-699

  • DOI: 10.1038/nchembio.117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The clinical success of multitargeted kinase inhibitors has stimulated efforts to identify promiscuous drugs with optimal selectivity profiles. It remains unclear to what extent such drugs can be rationally designed, particularly for combinations of ...

    The clinical success of multitargeted kinase inhibitors has stimulated efforts to identify promiscuous drugs with optimal selectivity profiles. It remains unclear to what extent such drugs can be rationally designed, particularly for combinations of targets that are structurally divergent. Here we report the systematic discovery of molecules that potently inhibit both tyrosine kinases and phosphatidylinositol-3-OH kinases, two protein families that are among the most intensely pursued cancer drug targets. Through iterative chemical synthesis, X-ray crystallography and kinome-level biochemical profiling, we identified compounds that inhibit a spectrum of new target combinations in these two families. Crystal structures revealed that the dual selectivity of these molecules is controlled by a hydrophobic pocket conserved in both enzyme classes and accessible through a rotatable bond in the drug skeleton. We show that one compound, PP121, blocks the proliferation of tumor cells by direct inhibition of oncogenic tyrosine kinases and phosphatidylinositol-3-OH kinases. These molecules demonstrate the feasibility of accessing a chemical space that intersects two families of oncogenes.


    Organizational Affiliation

    Program in Chemistry and Chemical Biology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
959Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153
Find proteins for P48736 (Homo sapiens)
Go to Gene View: PIK3CG
Go to UniProtKB:  P48736
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPZ
Query on NPZ

Download SDF File 
Download CCD File 
A
1-methyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C16 H13 N5
UOKGZPYGRJDACN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NPZKi: 570 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.302α = 90.00
b = 68.244β = 95.19
c = 106.069γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance