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 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/ml300309h
  • Primary Citation of Related Structures:  
    3ML8, 3ML9, 4HVB

  • 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 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:  (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 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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
19P
Query on 19P

Download Ideal Coordinates CCD File 
B [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
19P BindingDB:  4HVB Ki: 0.11 (nM) from 1 assay(s)
PDBBind:  4HVB Ki: 0.11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.333 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.8α = 90
b = 67.584β = 95.48
c = 106.897γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations