4EZJ

Potent and Selective Inhibitors of PI3K-delta: Obtaining Isoform Selectivity from the Affinity Pocket and Tryptophan Shelf

• PDB DOI: https://doi.org/10.2210/pdb4EZJ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-05-02 Released: 2013-04-17 
• Deposition Author(s): Murray, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.268 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Potent and selective inhibitors of PI3K-delta: obtaining isoform selectivity from the affinity pocket and tryptophan shelf

Sutherlin, D.P., Baker, S., Bisconte, A., Blaney, P.M., Brown, A., Chan, B.K., Chantry, D., Castanedo, G., DePledge, P., Goldsmith, P., Goldstein, D.M., Hancox, T., Kaur, J., Knowles, D., Kondru, R., Lesnick, J., Lucas, M.C., Lewis, C., Murray, J., Nadin, A.J., Nonomiya, J., Pang, J., Pegg, N., Price, S., Reif, K., Safina, B.S., Salphati, L., Staben, S., Seward, E.M., Shuttleworth, S., Sohal, S., Sweeney, Z.K., Ultsch, M., Waszkowycz, B., Wei, B.

(2012) Bioorg Med Chem Lett 22: 4296-4302

• PubMed: 22672799 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.027
• Primary Citation of Related Structures:  
  4EZJ, 4EZK, 4EZL


• PubMed Abstract: 
  

  A potent inhibitor of PI3Kδ that is ≥ 200 fold selective for the remaining three Class I PI3K isoforms and additional kinases is described. The hypothesis for selectivity is illustrated through structure activity relationships and crystal structures of compounds bound to a K802T mutant of PI3Kγ. Pharmacokinetic data in rats and mice support the use of 3 as a useful tool compound to use for in vivo studies.

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Organizational Affiliation: 

Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. [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: 111.2 kDa 
• Atom Count: 6,831 
• Modelled Residue Count: 834 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 1  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0SC	B [auth A]	2-(1-{[2-(5-fluoro-1H-indol-4-yl)-4-(morpholin-4-yl)pyrido[3,2-d]pyrimidin-6-yl]methyl}piperidin-4-yl)propan-2-ol C28 H33 F N6 O2 ONEJEIKQLAZPNN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0SC	PDBBind:  4EZJ	IC50: 3.8 (nM) from 1 assay(s)
	BindingDB:  4EZJ	IC50: 1585 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.268 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.2	α = 90
b = 67.12	β = 97.03
c = 104.77	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Murray, J.M.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description