1E8Y | pdb_00001e8y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.305 (Depositor), 0.304 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1E8Y

This is version 1.3 of the entry. See complete history

Literature

Structural Determinations 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.Whymann, M.P.Williams, R.L.

(2000) Mol Cell 6: 909

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


  • Organizational Affiliation
    • MRC Laboratory of Molecular Biology, MRC Centre, Cambridge, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 110.76 kDa 
  • Atom Count: 6,963 
  • Modeled Residue Count: 841 
  • Deposited Residue Count: 966 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT966Homo sapiensMutation(s): 0 
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt), 2.7.1.153 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.305 (Depositor), 0.304 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.227α = 90
b = 66.255β = 97.85
c = 102.642γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description