4J6I

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2013.02.102
  • Primary Citation of 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.


  • Organizational Affiliation

    Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. stevents@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): 0 
Gene Names: p110 gammaPIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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
1JV
Query on 1JV

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
1JV BindingDB:  4J6I IC50: 1.4 (nM) from 1 assay(s)
PDBBind:  4J6I IC50: 1.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.671α = 90
b = 67.161β = 95.43
c = 106.655γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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