Crystal structure of PI3K-alpha in complex with taselisib

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Discovery of GDC-0077 (Inavolisib), a Highly Selective Inhibitor and Degrader of Mutant PI3K alpha.

Hanan, E.J.Braun, M.G.Heald, R.A.MacLeod, C.Chan, C.Clausen, S.Edgar, K.A.Eigenbrot, C.Elliott, R.Endres, N.Friedman, L.S.Gogol, E.Gu, X.H.Thibodeau, R.H.Jackson, P.S.Kiefer, J.R.Knight, J.D.Nannini, M.Narukulla, R.Pace, A.Pang, J.Purkey, H.E.Salphati, L.Sampath, D.Schmidt, S.Sideris, S.Song, K.Sujatha-Bhaskar, S.Ultsch, M.Wallweber, H.Xin, J.Yeap, S.Young, A.Zhong, Y.Staben, S.T.

(2022) J Med Chem 65: 16589-16621

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01422
  • Primary Citation of Related Structures:  
    8EXL, 8EXO, 8EXU, 8EXV

  • PubMed Abstract: 

    Small molecule inhibitors that target the phosphatidylinositol 3-kinase (PI3K) signaling pathway have received significant interest for the treatment of cancers. The class I isoform PI3Kα is most commonly associated with solid tumors via gene amplification or activating mutations. However, inhibitors demonstrating both PI3K isoform and mutant specificity have remained elusive. Herein, we describe the optimization and characterization of a series of benzoxazepin-oxazolidinone ATP-competitive inhibitors of PI3Kα which also induce the selective degradation of the mutant p110α protein, the catalytic subunit of PI3Kα. Structure-based design informed isoform-specific interactions within the binding site, leading to potent inhibitors with greater than 300-fold selectivity over the other Class I PI3K isoforms. Further optimization of pharmacokinetic properties led to excellent in vivo exposure and efficacy and the identification of clinical candidate GDC-0077 (inavolisib, 32 ), which is now under evaluation in a Phase III clinical trial as a treatment for patients with PIK3CA -mutant breast cancer.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform1,080Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
799 (Subject of Investigation/LOI)
Query on 799

Download Ideal Coordinates CCD File 
B [auth A]2-methyl-2-(4-{2-[3-methyl-1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}-1H-pyrazol-1-yl)propanamide
C24 H28 N8 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.365α = 90
b = 134.385β = 90
c = 141.693γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-01-04
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Data collection