3TL5

Discovery of GDC-0980: a Potent, Selective, and Orally Available Class I Phosphatidylinositol 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Kinase Inhibitor for the Treatment of Cancer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.788 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent, Selective, and Orally Available Class I Phosphatidylinositol 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Kinase Inhibitor (GDC-0980) for the Treatment of Cancer.

Sutherlin, D.P.Bao, L.Berry, M.Castanedo, G.Chuckowree, I.Dotson, J.Folks, A.Friedman, L.Goldsmith, R.Gunzner, J.Heffron, T.Lesnick, J.Lewis, C.Mathieu, S.Murray, J.Nonomiya, J.Pang, J.Pegg, N.Prior, W.W.Rouge, L.Salphati, L.Sampath, D.Tian, Q.Tsui, V.Wan, N.C.Wang, S.Wei, B.Wiesmann, C.Wu, P.Zhu, B.Y.Olivero, A.

(2011) J.Med.Chem. 54: 7579-7587

  • DOI: 10.1021/jm2009327

  • PubMed Abstract: 
  • The discovery of 2 (GDC-0980), a class I PI3K and mTOR kinase inhibitor for oncology indications, is described. mTOR inhibition was added to the class I PI3K inhibitor 1 (GDC-0941) scaffold primarily through the substitution of the indazole in 1 for ...

    The discovery of 2 (GDC-0980), a class I PI3K and mTOR kinase inhibitor for oncology indications, is described. mTOR inhibition was added to the class I PI3K inhibitor 1 (GDC-0941) scaffold primarily through the substitution of the indazole in 1 for a 2-aminopyrimidine. This substitution also increased the microsomal stability and the free fraction of compounds as evidenced through a pairwise comparison of molecules that were otherwise identical. Highlighted in detail are analogues of an advanced compound 4 that were designed to improve solubility, resulting in 2. This compound, is potent across PI3K class I isoforms with IC(50)s of 5, 27, 7, and 14 nM for PI3Kα, β, δ, and γ, respectively, inhibits mTOR with a K(i) of 17 nM yet is highly selective versus a large panel of kinases including others in the PIKK family. On the basis of the cell potency, low clearance in mouse, and high free fraction, 2 demonstrated significant efficacy in mouse xenografts when dosed as low as 1 mg/kg orally and is currently in phase I clinical trials for cancer.


    Organizational Affiliation

    Genentech, Inc., South San Francisco, CA 94080, USA. sutherlin.dan@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
A
966Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153
Find proteins for P48736 (Homo sapiens)
Go to Gene View: PIK3CG
Go to UniProtKB:  P48736
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
980
Query on 980

Download SDF File 
Download CCD File 
A
(2S)-1-(4-{[2-(2-aminopyrimidin-5-yl)-7-methyl-4-(morpholin-4-yl)thieno[3,2-d]pyrimidin-6-yl]methyl}piperazin-1-yl)-2-hydroxypropan-1-one
C23 H30 N8 O3 S
YOVVNQKCSKSHKT-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
980IC50: 14 - 36 nM (100) BINDINGDB
980IC50: 14 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.788 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 140.865α = 90.00
b = 67.012β = 96.77
c = 105.812γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references