4XE0

Idelalisib bound to the p110 subunit of PI3K delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.434 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural, Biochemical, and Biophysical Characterization of Idelalisib Binding to Phosphoinositide 3-Kinase delta.

Somoza, J.R.Koditek, D.Villasenor, A.G.Novikov, N.Wong, M.H.Liclican, A.Xing, W.Lagpacan, L.Wang, R.Schultz, B.E.Papalia, G.A.Samuel, D.Lad, L.McGrath, M.E.

(2015) J.Biol.Chem. 290: 8439-8446

  • DOI: 10.1074/jbc.M114.634683

  • PubMed Abstract: 
  • Idelalisib (also known as GS-1101, CAL-101, IC489666, and Zydelig) is a PI3Kδ inhibitor that has recently been approved for the treatment of several hematological malignancies. Given its use in human diseases, we needed a clear picture of how idelali ...

    Idelalisib (also known as GS-1101, CAL-101, IC489666, and Zydelig) is a PI3Kδ inhibitor that has recently been approved for the treatment of several hematological malignancies. Given its use in human diseases, we needed a clear picture of how idelalisib binds to and inhibits PI3Kδ. Our data show that idelalisib is a potent and selective inhibitor of the kinase activity of PI3Kδ. A kinetic characterization clearly demonstrated ATP-competitive inhibition, and several additional biochemical and biophysical assays showed that the compound binds reversibly and noncovalently to the kinase. A crystal structure of idelalisib bound to the p110δ subunit of PI3Kδ furthers our understanding of the binding interactions that confer the potency and selectivity of idelalisib.


    Organizational Affiliation

    From the Departments of Structural Chemistry and john.somoza@gilead.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
A
939Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
Find proteins for O35904 (Mus musculus)
Go to UniProtKB:  O35904
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
40L
Query on 40L

Download SDF File 
Download CCD File 
A
5-fluoro-3-phenyl-2-[(1S)-1-(7H-purin-6-ylamino)propyl]quinazolin-4(3H)-one
C22 H18 F N7 O
IFSDAJWBUCMOAH-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
40LIC50: 2.5 - 25 nM (94) BINDINGDB
40LIC50: 19 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.434 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.049α = 90.00
b = 64.590β = 103.09
c = 115.960γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOSFLMdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references
  • Version 1.2: 2015-04-08
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Database references, Derived calculations, Source and taxonomy