1E7V

Structure determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin and staurosporine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine.

Walker, E.H.Pacold, M.E.Perisic, O.Stephens, L.Hawkins, P.T.Wymann, M.P.Williams, R.L.

(2000) Mol Cell 6: 909-919

  • DOI: 10.1016/s1097-2765(05)00089-4
  • Primary Citation of Related Structures:  
    1E7V, 1E7U, 1E8Z, 1E8Y, 1E8X, 1E8W, 1E90

  • PubMed Abstract: 
  • The specific phosphoinositide 3-kinase (PI3K) inhibitors wortmannin and LY294002 have been invaluable tools for elucidating the roles of these enzymes in signal transduction pathways. The X-ray crystallographic structures of PI3Kgamma bound to these ...

    The specific phosphoinositide 3-kinase (PI3K) inhibitors wortmannin and LY294002 have been invaluable tools for elucidating the roles of these enzymes in signal transduction pathways. The X-ray crystallographic structures of PI3Kgamma bound to these lipid kinase inhibitors and to the broad-spectrum protein kinase inhibitors quercetin, myricetin, and staurosporine reveal how these compounds fit into the ATP binding pocket. With a nanomolar IC50, wortmannin most closely fits and fills the active site and induces a conformational change in the catalytic domain. Surprisingly, LY294002 and the lead compound on which it was designed, quercetin, as well as the closely related flavonoid myricetin bind PI3K in remarkably different orientations that are related to each other by 180 degrees rotations. Staurosporine/PI3K interactions are reminiscent of low-affinity protein kinase/staurosporine complexes. These results provide a rich basis for development of isoform-specific PI3K inhibitors with therapeutic potential.


    Related Citations: 
    • Structural Insights Into Phosphoinositide 3-Kinase Catalysis and Signalling
      Walker, E.H., Perisic, O., Ried, C., Stephens, L., Williams, R.L.
      (1999) Nature 402: 313

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, MRC Centre, Cambridge, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNITA961Sus scrofaMutation(s): 0 
Gene Names: P120S144CPIK3CG
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (UniProt), 2.7.11.1 (UniProt)
Find proteins for O02697 (Sus scrofa)
Explore O02697 
Go to UniProtKB:  O02697
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LY2
Query on LY2

Download CCD File 
A
2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE
C19 H17 N O3
CZQHHVNHHHRRDU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LY2Kd:  210   nM  BindingDB
LY2IC50:  1775   nM  BindingDB
LY2IC50:  7200   nM  BindingDB
LY2IC50:  7260   nM  BindingDB
LY2IC50:  7300   nM  BindingDB
LY2IC50:  1600   nM  BindingDB
LY2IC50:  1720   nM  BindingDB
LY2IC50:  6600   nM  BindingDB
LY2IC50:  1500   nM  BindingDB
LY2IC50:  1400   nM  BindingDB
LY2IC50:  1060   nM  BindingDB
LY2IC50:  1200   nM  BindingDB
LY2IC50:  947   nM  BindingDB
LY2IC50:  3020   nM  BindingDB
LY2IC50:  12000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.826α = 90
b = 67.334β = 96.13
c = 106.257γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-17
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references, Other