3NZU

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

• PDB DOI: https://doi.org/10.2210/pdb3NZU/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-07-16 Released: 2010-12-29 
• Deposition Author(s): Murray, J.M., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 

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

• PubMed: 20822905 
• 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.

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Organizational Affiliation: 

Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.77 kDa 
• Atom Count: 6,697 
• Modelled Residue Count: 822 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	954	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NZU	B [auth A]	6-(2H-indazol-4-yl)-1-methyl-N-[3-(methylsulfonyl)propyl]-1H-pyrazolo[3,4-d]pyrimidin-4-amine C17 H19 N7 O2 S YZTXAMRYFBNCHP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NZU	PDBBind:  3NZU	IC50: 1.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.213 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.004	α = 90
b = 67.677	β = 95.52
c = 106.362	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Murray, J.M., Wiesmann, C.

Revision History  

• 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