4J6I | pdb_00004j6i

Discovery of thiazolobenzoxepin PI3-kinase inhibitors that spare the PI3-kinase beta isoform

• PDB DOI: https://doi.org/10.2210/pdb4J6I/pdb

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


• Deposited: 2013-02-11 Released: 2013-08-28 
• Deposition Author(s): Murray, J.M., Rouge, L., Wu, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Discovery of thiazolobenzoxepin PI3-kinase inhibitors that spare the PI3-kinase beta isoform.

Staben, S.T., Ndubaku, C., Blaquiere, N., Belvin, M., Bull, R.J., Dudley, D., Edgar, K., Gray, D., Heald, R., Heffron, T.P., Jones, G.E., Jones, M., Kolesnikov, A., Lee, L., Lesnick, J., Lewis, C., Murray, J., McLean, N.J., Nonomiya, J., Olivero, A.G., Ord, R., Pang, J., Price, S., Prior, W.W., Rouge, L., Salphati, L., Sampath, D., Wallin, J., Wang, L., Wei, B., Weismann, C., Wu, P.

(2013) Bioorg Med Chem Lett 23: 2606-2613

• PubMed: 23540645 
• DOI: https://doi.org/10.1016/j.bmcl.2013.02.102
• Primary Citation Related Structures: 
  4J6I


• PubMed Abstract: 
  

  A series of suitable five-membered heterocyclic alternatives to thiophenes within a thienobenzoxepin class of PI3-kinase (PI3K) inhibitors was discovered. Specific thiazolobenzoxepin 8-substitution was identified that increased selectivity over PI3Kβ. PI3Kβ-sparing compound 27 (PI3Kβ Ki,app/PI3Kα Ki,app=57) demonstrated dose-dependent knockdown of pAKT, pPRAS40 and pS6RP in vivo as well as differential effects in an in vitro proliferation cell line screen compared to pan PI3K inhibitor GDC-0941. A new structure-based hypothesis for reducing inhibition of the PI3K β isoform while maintaining activity against α, δ and γ isoforms is presented.

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Organizational Affiliation: 
• Discovery Chemistry, 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: 111.22 kDa 
• Atom Count: 6,783 
• Modeled Residue Count: 833 
• 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): 0  Gene Names: p110 gamma, 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
1JV	B [auth A]	2-methyl-1-(4-{2-[1-(2,2,2-trifluoroethyl)-1H-1,2,4-triazol-5-yl]-4,5-dihydro[1]benzoxepino[5,4-d][1,3]thiazol-8-yl}-1H-pyrazol-1-yl)propan-2-ol C22 H21 F3 N6 O2 S VRJUJTMBOARYOG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.251 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.671	α = 90
b = 67.161	β = 95.43
c = 106.655	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Murray, J.M., Rouge, L., Wu, P.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations