Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 291.29 kDa 
• Atom Count: 18333 
• Modelled Residue Count: 2216 
• Deposited Residue Count: 2472 
• Unique protein chains: 2

5DXH

p110alpha/p85alpha with compound 5

• PDB DOI: 10.2210/pdb5DXH/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-09-23 Released: 2016-01-27 
• Deposition Author(s): Heffron, T.P., Heald, R.A., Ndubaku, C., Wei, B.Q., Augustin, 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., Mortle, M., Nonomiya, J., Pang, J., Price, S., Prior, W.W., Salphati, L., Sideris, S., Staben, S., Steinbacher, S., Tsui, V., Wallin, J., Sampath, D., Olivero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

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

• PubMed: 26741947 
• 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 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).

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A, C [auth D]	1067	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B, D [auth E]	169	Bos taurus	Mutation(s): 0  Gene Names: PIK3R1
UniProt
Find proteins for P23727 (Bos taurus) Explore P23727  Go to UniProtKB:  P23727

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5H2	E [auth A], F [auth D]	methyl {2-[4-(2-chlorophenyl)-4H-1,2,4-triazol-3-yl]-4,5-dihydrothieno[3,2-d][1]benzoxepin-8-yl}carbamate C22 H17 Cl N4 O3 S IMSBGZSMSGCJBM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5H2	BindingDB:  5DXH	Ki: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.66	α = 90
b = 121.83	β = 102.33
c = 166.36	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-09-23 
• Released Date: 2016-01-27 
Deposition Author(s): Heffron, T.P., Heald, R.A., Ndubaku, C., Wei, B.Q., Augustin, 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., Mortle, M., Nonomiya, J., Pang, J., Price, S., Prior, W.W., Salphati, L., Sideris, S., Staben, S., Steinbacher, S., Tsui, V., Wallin, J., Sampath, D., Olivero, A.

Revision History  

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