3P2B | pdb_00003p2b

Crystal Structure of PI3K gamma with 3-(2-morpholino-6-(pyridin-3-ylamino)pyrimidin-4-yl)phenol

• PDB DOI: https://doi.org/10.2210/pdb3P2B/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-10-01 Released: 2011-08-17 
• Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.263 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Identification and structure-activity relationship of 2-morpholino 6-(3-hydroxyphenyl) pyrimidines, a class of potent and selective PI3 kinase inhibitors.

Pecchi, S., Renhowe, P.A., Taylor, C., Kaufman, S., Merritt, H., Wiesmann, M., Shoemaker, K.R., Knapp, M.S., Ornelas, E., Hendrickson, T.F., Fantl, W., Voliva, C.F.

(2010) Bioorg Med Chem Lett 20: 6895-6898

• PubMed: 21035331 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.021
• Primary Citation Related Structures: 
  3P2B


• PubMed Abstract: 
  

  PI3 Kinases are a family of lipid kinases mediating numerous cell processes such as proliferation, migration, and differentiation. The PI3 kinase pathway is often de-regulated in cancer through PI3Kα overexpression, gene amplification, mutations, and PTEN phosphatase deletion. PI3K inhibitors represent therefore an attractive therapeutic modality for cancer treatment. Herein we describe a novel series of PI3K inhibitors sharing a pyrimidine core and showing significant potency against class I PI3 kinases in the biochemical assay and in cells. The discovery, synthesis and SAR of this chemotype are described.

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Organizational Affiliation: 
• Novartis Institutes for Biomedical Research, Emeryville, CA, 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: 111.11 kDa 
• Atom Count: 6,435 
• Modeled Residue Count: 808 
• Deposited Residue Count: 966 
• 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	966	Homo sapiens	Mutation(s): 1  Gene Names: PIK3CG, PK3CG 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
P2B	B [auth A]	3-[2-morpholin-4-yl-6-(pyridin-3-ylamino)pyrimidin-4-yl]phenol C19 H19 N5 O2 VPAXYWZGMCIWNR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.263 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.12	α = 90
b = 66.78	β = 96.95
c = 105.97	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BOS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-17 
Deposition Author(s): Knapp, M.S., Elling, R.A., Ornelas, E.

Revision History  

• Version 1.0: 2011-08-17
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations