5DXT

p110alpha with GDC-0326


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Rational Design of Selective Benzoxazepin Inhibitors of the alpha-Isoform of Phosphoinositide 3-Kinase Culminating in the Identification of (S)-2-((2-(1-Isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepin-9-yl)oxy)propanamide (GDC-0326).

Heffron, T.P.Heald, R.A.Ndubaku, C.Wei, B.Augistin, M.Do, S.Edgar, K.Eigenbrot, C.Friedman, L.Gancia, E.Jackson, P.S.Jones, G.Kolesnikov, A.Lee, L.B.Lesnick, J.D.Lewis, C.McLean, N.Mortl, M.Nonomiya, J.Pang, J.Price, S.Prior, W.W.Salphati, L.Sideris, S.Staben, S.T.Steinbacher, S.Tsui, V.Wallin, J.Sampath, D.Olivero, A.G.

(2016) J Med Chem 59: 985-1002

  • DOI: 10.1021/acs.jmedchem.5b01483
  • Primary Citation of Related Structures:  
    5DXH, 5DXT, 5DXU

  • PubMed Abstract: 
  • Inhibitors of the class I phosphoinositide 3-kinase (PI3K) isoform PI3Kα have received substantial attention for their potential use in cancer therapy. Despite the particular attraction of targeting PI3Kα, achieving selectivity for the inhibition of this ...

    Inhibitors of the class I phosphoinositide 3-kinase (PI3K) isoform PI3Kα have received substantial attention for their potential use in cancer therapy. Despite the particular attraction of targeting PI3Kα, achieving selectivity for the inhibition of this isoform has proved challenging. Herein we report the discovery of inhibitors of PI3Kα that have selectivity over the other class I isoforms and all other kinases tested. In GDC-0032 (3, taselisib), we previously minimized inhibition of PI3Kβ relative to the other class I insoforms. Subsequently, we extended our efforts to identify PI3Kα-specific inhibitors using PI3Kα crystal structures to inform the design of benzoxazepin inhibitors with selectivity for PI3Kα through interactions with a nonconserved residue. Several molecules selective for PI3Kα relative to the other class I isoforms, as well as other kinases, were identified. Optimization of properties related to drug metabolism then culminated in the identification of the clinical candidate GDC-0326 (4).


    Organizational Affiliation

    Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform A962Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
NIH Common Fund Data Resources
PHAROS:  P42336
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5H5
Query on 5H5

Download Ideal Coordinates CCD File 
A
(2S)-2-({2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}oxy)propanamide
C19 H22 N6 O3
SIKYDKLGPWRPMZ-LBPRGKRZSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5H5Ki:  0.20000000298023224   nM  Binding MOAD
5H5Ki:  0.20000000298023224   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.507α = 90
b = 133.672β = 90
c = 141.339γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references