4FUL | pdb_00004ful

PI3 Kinase Gamma bound to a pyrmidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4FUL/pdb

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


• Deposited: 2012-06-28 Released: 2012-10-17 
• Deposition Author(s): Gopalsamy, A., Bennett, E.M., Shi, M., Zhang, W.G., Bard, J., Yu, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Identification of pyrimidine derivatives as hSMG-1 inhibitors.

Gopalsamy, A., Bennett, E.M., Shi, M., Zhang, W.G., Bard, J., Yu, K.

(2012) Bioorg Med Chem Lett 22: 6636-6641

• PubMed: 23021994 
• DOI: https://doi.org/10.1016/j.bmcl.2012.08.107
• Primary Citation Related Structures: 
  4FUL


• PubMed Abstract: 
  

  hSMG-1 kinase plays a dual role in a highly conserved RNA surveillance pathway termed nonsense-mediated RNA decay (NMD) and in cellular genotoxic stress response. Since deregulation of cellular responses to stress contributes to tumor growth and resistance to chemotherapy, hSMG-1 is a potential target for cancer treatment. From our screening efforts, we have identified pyrimidine derivatives as hSMG-1 kinase inhibitors. We report structure-based optimization of this pan-kinase scaffold to improve its biochemical profile and overall kinome selectivity, including mTOR and CDK, to generate the first reported selective hSMG-1 tool compound.

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Organizational Affiliation: 
• Worldwide Medicinal Chemistry, Pfizer, 200 Cambridgepark Drive, Cambridge, MA 02140, 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: 111.19 kDa 
• Atom Count: 6,846 
• Modeled Residue Count: 832 
• 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
0VU	B [auth A]	4-({4-[3-(piperidin-1-ylcarbonyl)phenyl]pyrimidin-2-yl}amino)benzenesulfonamide C22 H23 N5 O3 S AMGRGTYETFMYTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.261 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.04	α = 90
b = 66.9	β = 97.59
c = 102.82	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Gopalsamy, A., Bennett, E.M., Shi, M., Zhang, W.G., Bard, J., Yu, K.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary