3L13

Crystal Structures of Pan-PI3-Kinase and Dual Pan-PI3-Kinase/mTOR Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of (Thienopyrimidin-2-yl)aminopyrimidines as Potent, Selective, and Orally Available Pan-PI3-Kinase and Dual Pan-PI3-Kinase/mTOR Inhibitors for the Treatment of Cancer.

Sutherlin, D.P.Sampath, D.Berry, M.Castanedo, G.Chang, Z.Chuckowree, I.Dotson, J.Folkes, A.Friedman, L.Goldsmith, R.Heffron, T.Lee, L.Lesnick, J.Lewis, C.Mathieu, S.Nonomiya, J.Olivero, A.Pang, J.Prior, W.W.Salphati, L.Sideris, S.Tian, Q.Tsui, V.Wan, N.C.Wang, S.Wiesmann, C.Wong, S.Zhu, B.Y.

(2010) J Med Chem 53: 1086-1097

  • DOI: https://doi.org/10.1021/jm901284w
  • Primary Citation of Related Structures:  
    3L13, 3L16, 3L17

  • PubMed Abstract: 

    The PI3K/AKT/mTOR pathway has been shown to play an important role in cancer. Starting with compounds 1 and 2 (GDC-0941) as templates, (thienopyrimidin-2-yl)aminopyrimidines were discovered as potent inhibitors of PI3K or both PI3K and mTOR. Structural information derived from PI3K gamma-ligand cocrystal structures of 1 and 2 were used to design inhibitors that maintained potency for PI3K yet improved metabolic stability and oral bioavailability relative to 1. The addition of a single methyl group to the optimized 5 resulted in 21, which had significantly reduced potency for mTOR. The lead compounds 5 (GNE-493) and 21 (GNE-490) have good pharmacokinetic (PK) parameters, are highly selective, demonstrate knock down of pathway markers in vivo, and are efficacious in xenograft models where the PI3K pathway is deregulated. Both compounds were compared in a PI3K alpha mutated MCF7.1 xenograft model and were found to have equivalent efficacy when normalized for exposure.


  • Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, California 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 isoform960Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt)
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
JZW
Query on JZW

Download Ideal Coordinates CCD File 
B [auth A][3-(6-{[4-(methylsulfonyl)piperazin-1-yl]methyl}-4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenyl]methanol
C23 H29 N5 O4 S2
UTNWCQOGZIRULH-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JZW BindingDB:  3L13 IC50: 15 (nM) from 1 assay(s)
PDBBind:  3L13 IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.359α = 90
b = 67.741β = 95.63
c = 107.151γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
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: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description