RCSB PDB - 3NZS: Structure-based Optimization of Pyrazolo -Pyrimidine and -Pyridine Inhibitors of PI3-Kinase

 3NZS

Structure-based Optimization of Pyrazolo -Pyrimidine and -Pyridine Inhibitors of PI3-Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NZSClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-based optimization of pyrazolo-pyrimidine and -pyridine inhibitors of PI3-kinase.

Staben, S.T.Heffron, T.P.Sutherlin, D.P.Bhat, S.R.Castanedo, G.M.Chuckowree, I.S.Dotson, J.Folkes, A.J.Friedman, L.S.Lee, L.Lesnick, J.Lewis, C.Murray, J.M.Nonomiya, J.Olivero, A.G.Plise, E.Pang, J.Prior, W.W.Salphati, L.Rouge, L.Sampath, D.Tsui, V.Wan, N.C.Wang, S.Wiesmann, C.Wu, P.Zhu, B.Y.

(2010) Bioorg Med Chem Lett 20: 6048-6051

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.067
  • Primary Citation of Related Structures:  
    3NZS, 3NZU

  • PubMed Abstract: 

    Starting from HTS hit 1a, X-ray co-crystallization and molecular modeling were used to design potent and selective inhibitors of PI3-kinase. Bioavailablity in this series was improved through careful modulation of physicochemical properties. Compound 12 displayed in vivo knockdown of PI3K pharmacodynamic markers such as pAKT, pPRAS40, and pS6RP in a PC3 prostate cancer xenograft model.


  • Organizational Affiliation

    Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, USA. stevents@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 isoform954Homo 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
NZS
Query on NZS

Download Ideal Coordinates CCD File 
B [auth A]6-(1,1-dioxidothiomorpholin-4-yl)-N-(3-methoxyphenyl)-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C17 H20 N6 O3 S
IDYJWHSIWMIDKD-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NZS PDBBind:  3NZS IC50: 75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.966α = 90
b = 67.965β = 95.57
c = 106.989γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NZSClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations