4HVB

Catalytic unit of PI3Kg in complex with PI3K/mTOR dual inhibitor PF-04979064


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of the Highly Potent PI3K/mTOR Dual Inhibitor PF-04979064 through Structure-Based Drug Design.

Cheng, H.Li, C.Bailey, S.Baxi, S.M.Goulet, L.Guo, L.Hoffman, J.Jiang, Y.Johnson, T.O.Johnson, T.W.Knighton, D.R.Li, J.Liu, K.K.Liu, Z.Marx, M.A.Walls, M.Wells, P.A.Yin, M.J.Zhu, J.Zientek, M.

(2013) ACS Med Chem Lett 4: 91-97

  • DOI: 10.1021/ml300309h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PI3K, AKT, and mTOR are key kinases from PI3K signaling pathway being extensively pursued to treat a variety of cancers in oncology. To search for a structurally differentiated back-up candidate to PF-04691502, which is currently in phase I/II clinic ...

    PI3K, AKT, and mTOR are key kinases from PI3K signaling pathway being extensively pursued to treat a variety of cancers in oncology. To search for a structurally differentiated back-up candidate to PF-04691502, which is currently in phase I/II clinical trials for treating solid tumors, a lead optimization effort was carried out with a tricyclic imidazo[1,5]naphthyridine series. Integration of structure-based drug design and physical properties-based optimization yielded a potent and selective PI3K/mTOR dual kinase inhibitor PF-04979064. This manuscript discusses the lead optimization for the tricyclic series, which both improved the in vitro potency and addressed a number of ADMET issues including high metabolic clearance mediated by both P450 and aldehyde oxidase (AO), poor permeability, and poor solubility. An empirical scaling tool was developed to predict human clearance from in vitro human liver S9 assay data for tricyclic derivatives that were AO substrates.


    Organizational Affiliation

    Cancer Chemistry, PDM, and Oncology Research Unit, Pfizer Worldwide Research and Development , La Jolla Laboratories, 10770 Science Center Drive, San Diego, California 92121, United States.




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
19P
Query on 19P

Download SDF File 
Download CCD File 
A
1-{1-[(2S)-2-hydroxypropanoyl]piperidin-4-yl}-3-methyl-8-(6-methylpyridin-3-yl)-1,3-dihydro-2H-imidazo[4,5-c][1,5]naphthyridin-2-one
C24 H26 N6 O3
GACQNUHFDBEIQH-HNNXBMFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
19PKi: 0.1 nM (99) BINDINGDB
19PKi: 0.111 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.270 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.800α = 90.00
b = 67.584β = 95.48
c = 106.897γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNXrefinement
CNXphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references