4FAD

Design and Synthesis of a Novel Pyrrolidinyl Pyrido Pyrimidinone Derivative as a Potent Inhibitor of PI3Ka and mTOR

• PDB DOI: https://doi.org/10.2210/pdb4FAD/pdb

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


• Deposited: 2012-05-22 Released: 2013-04-03 
• Deposition Author(s): Greasley, S.E., Knighton, D.R., LaFleur Rogers, C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.262 
• R-Value Observed: 0.262 

Literature

Design and synthesis of a novel pyrrolidinyl pyrido pyrimidinone derivative as a potent inhibitor of PI3Kalpha and mTOR

Le, P.T., Cheng, H., Ninkovic, S., Plewe, M., Huang, X., Wang, H., Bagrodia, S., Sun, S., Knighton, D.R., LaFleur Rogers, C.M., Pannifer, A., Greasley, S., Dalvie, D., Zhang, E.

(2012) Bioorg Med Chem Lett 22: 5098-5103

• PubMed: 22749419 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.100
• Primary Citation of Related Structures:  
  4FA6, 4FAD


• PubMed Abstract: 
  

  Lead optimization efforts that employed structure base drug design and physicochemical property based optimization leading to the discovery of a novel series of 4-methylpyrido pyrimidinone (MPP) are discussed. Synthesis and profile of 1, a PI3Kα/mTOR dual inhibitor, is highlighted.

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Organizational Affiliation: 

Cancer Chemistry, Pfizer Worldwide Research & Development, La Jolla Laboratories, Pfizer Inc., La Jolla, CA 92121, United States. [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: 111.1 kDa 
• Atom Count: 6,813 
• Modelled Residue Count: 839 
• 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): 0  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (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
0TB	B [auth A]	2-amino-6-(5-fluoro-6-methoxypyridin-3-yl)-4-methyl-8-(pyrrolidin-1-yl)pyrido[2,3-d]pyrimidin-7(8H)-one C18 H19 F N6 O2 YJFBSFMYXTWDGD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.265 
• R-Value Work: 0.262 
• R-Value Observed: 0.262 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.55	α = 90
b = 67.26	β = 95.68
c = 107.6	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Greasley, S.E., Knighton, D.R., LaFleur Rogers, C.M.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations