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: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm2009327
  • Primary Citation of Related Structures:  
    3TL5

  • 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 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:  (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: PIK3CG
EC: 2.7.1.153
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
980
Query on 980

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
980 BindingDB:  3TL5 Kd: 2.6 (nM) from 1 assay(s)
IC50: min: 14, max: 36 (nM) from 2 assay(s)
PDBBind:  3TL5 IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.865α = 90
b = 67.012β = 96.77
c = 105.812γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-16
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description