3CSF

Crystal structure of PI3K p110gamma catalytical domain in complex with organoruthenium inhibitor DW2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design of an organoruthenium phosphatidyl-inositol-3-kinase inhibitor reveals a switch governing lipid kinase potency and selectivity.

Xie, P.Williams, D.S.Atilla-Gokcumen, G.E.Milk, L.Xiao, M.Smalley, K.S.Herlyn, M.Meggers, E.Marmorstein, R.

(2008) Acs Chem.Biol. 3: 305-316

  • DOI: 10.1021/cb800039y
  • Primary Citation of Related Structures:  3CST

  • PubMed Abstract: 
  • Mutations that constitutively activate the phosphatidyl-inositol-3-kinase (PI3K) signaling pathway, including alterations in PI3K, PTEN, and AKT, are found in a variety of human cancers, implicating the PI3K lipid kinase as an attractive target for t ...

    Mutations that constitutively activate the phosphatidyl-inositol-3-kinase (PI3K) signaling pathway, including alterations in PI3K, PTEN, and AKT, are found in a variety of human cancers, implicating the PI3K lipid kinase as an attractive target for the development of therapeutic agents to treat cancer and other related diseases. In this study, we report on the combination of a novel organometallic kinase inhibitor scaffold with structure-based design to develop a PI3K inhibitor, called E5E2, with an IC 50 potency in the mid-low-nanomolar range and selectivity against a panel of protein kinases. We also show that E5E2 inhibits phospho-AKT in human melanoma cells and leads to growth inhibition. Consistent with a role for the PI3K pathway in tumor cell invasion, E5E2 treatment also inhibits the migration of melanoma cells in a 3D spheroid assay. The structure of the PI3Kgamma/E5E2 complex reveals the molecular features that give rise to this potency and selectivity toward lipid kinases with implications for the design of a subsequent generation of PI3K-isoform-specific organometallic inhibitors.


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
966Homo sapiensGene Names: PIK3CG
EC: 2.7.11.1, 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
DW2
Query on DW2

Download SDF File 
Download CCD File 
A
RU-PYRIDOCARBAZOLE-2
C23 H13 N3 O4 Ru
KERGYDCAYYYADM-UDLLLUGBCD
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.635α = 90.00
b = 68.082β = 95.26
c = 106.270γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description