4EZK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. sutherd1@gene.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform966Homo sapiensMutation(s): 1 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Membrane Entity: Yes 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0SD
Query on 0SD

Download Ideal Coordinates CCD File 
B [auth A]2-(1-{[2-(2H-indazol-4-yl)-4-(morpholin-4-yl)pyrido[3,2-d]pyrimidin-6-yl]methyl}piperidin-4-yl)propan-2-ol
C27 H33 N7 O2
YEOXTSXBPMKEQR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0SD PDBBind:  4EZK IC50: 6.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.73α = 90
b = 67.19β = 96.76
c = 106.02γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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