4FJZ

Crystal structure of PI3K-gamma in complex with pyrrolo-pyridine inhibitor 63

• PDB DOI: https://doi.org/10.2210/pdb4FJZ/pdb

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


• Deposited: 2012-06-12 Released: 2012-10-24 
• Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 

Literature

Discovery and in Vivo Evaluation of Dual PI3K-beta/delta inhibitors

Gonzalez-Lopez de Turiso, F., Shin, Y., Brown, M., Cardozo, M., Chen, Y., Fong, D., Hao, X., He, X., Henne, K., Hu, Y.L., Johnson, M.G., Kohn, T., Lohman, J., McBride, H.J., McGee, L.R., Medina, J.C., Metz, D., Miner, K., Mohn, D., Pattaropong, V., Seganish, J., Simard, J.L., Wannberg, S., Whittington, D.A., Yu, G., Cushing, T.D.

(2012) J Med Chem 55: 7667-7685

• PubMed: 22876881 
• DOI: https://doi.org/10.1021/jm300679u
• Primary Citation of Related Structures:  
  4FJY, 4FJZ


• PubMed Abstract: 
  

  Structure-based rational design led to the synthesis of a novel series of potent PI3K inhibitors. The optimized pyrrolopyridine analogue 63 was a potent and selective PI3Kβ/δ dual inhibitor that displayed suitable physicochemical properties and pharmacokinetic profile for animal studies. Analogue 63 was found to be efficacious in animal models of inflammation including a keyhole limpet hemocyanin (KLH) study and a collagen-induced arthritis (CIA) disease model of rheumatoid arthritis. These studies highlight the potential therapeutic value of inhibiting both the PI3Kβ and δ isoforms in the treatment of a number of inflammatory diseases.

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Organizational Affiliation: 

Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 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: 110.72 kDa 
• Atom Count: 6,726 
• Modelled Residue Count: 822 
• Deposited Residue Count: 960 
• 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	960	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4FJ	F [auth A]	1'-[7-fluoro-3-methyl-2-(pyridin-2-yl)quinolin-4-yl]-6'-(morpholin-4-yl)-1',2,2',3,5,6-hexahydrospiro[pyran-4,3'-pyrrolo[3,2-b]pyridine] C30 H30 F N5 O2 JZYCUVQYCHLFBL-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
4FJ	PDBBind:  4FJZ	Ki: 509 (nM) from 1 assay(s)
	BindingDB:  4FJZ	Ki: 509 (nM) from 1 assay(s)
		IC50: 825 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.280 
• R-Value Work: 0.203 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.313	α = 90
b = 67.899	β = 95.26
c = 106.306	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Whittington, D.A., Tang, J., Yakowec, P.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations