4XE0

Idelalisib bound to the p110 subunit of PI3K delta

• PDB DOI: https://doi.org/10.2210/pdb4XE0/pdb

• Classification: Transferase/transferase inhibitor
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-12-20 Released: 2015-02-04 
• Deposition Author(s): Somoza, J.R., Villasenor, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.289 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Starting Model: experimental

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

• PubMed: 25631052 
• DOI: https://doi.org/10.1074/jbc.M114.634683
• Primary Citation of Related Structures:  
  4XE0


• 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 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.

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Organizational Affiliation: 

From the Departments of Structural Chemistry and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.18 kDa 
• Atom Count: 6,821 
• Modelled Residue Count: 815 
• Deposited Residue Count: 939 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	939	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
40L	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
40L	BindingDB:  4XE0	IC50: min: 1, max: 831 (nM) from 30 assay(s)
		EC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 0.289 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.049	α = 90
b = 64.59	β = 103.09
c = 115.96	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Somoza, J.R., Villasenor, A.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-02-11
  Changes: Database references
• Version 1.2: 2015-04-08
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description