4FHJ

Crystal Structure of PI3K-gamma in Complex with Imidazopyridine 2

• PDB DOI: https://doi.org/10.2210/pdb4FHJ/pdb

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


• Deposited: 2012-06-06 Released: 2012-07-18 
• Deposition Author(s): Shaffer, P.L., Tang, J., Yakowec, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Discovery and optimization of potent and selective imidazopyridine and imidazopyridazine mTOR inhibitors.

Peterson, E.A., Boezio, A.A., Andrews, P.S., Boezio, C.M., Bush, T.L., Cheng, A.C., Choquette, D., Coats, J.R., Colletti, A.E., Copeland, K.W., Dupont, M., Graceffa, R., Grubinska, B., Kim, J.L., Lewis, R.T., Liu, J., Mullady, E.L., Potashman, M.H., Romero, K., Shaffer, P.L., Stanton, M.K., Stellwagen, J.C., Teffera, Y., Yi, S., Cai, T., La, D.S.

(2012) Bioorg Med Chem Lett 22: 4967-4974

• PubMed: 22765895 
• DOI: https://doi.org/10.1016/j.bmcl.2012.06.033
• Primary Citation of Related Structures:  
  4FHJ, 4FHK


• PubMed Abstract: 
  

  mTOR is a critical regulator of cellular signaling downstream of multiple growth factors. The mTOR/PI3K/AKT pathway is frequently mutated in human cancers and is thus an important oncology target. Herein we report the evolution of our program to discover ATP-competitive mTOR inhibitors that demonstrate improved pharmacokinetic properties and selectivity compared to our previous leads. Through targeted SAR and structure-guided design, new imidazopyridine and imidazopyridazine scaffolds were identified that demonstrated superior inhibition of mTOR in cellular assays, selectivity over the closely related PIKK family and improved in vivo clearance over our previously reported benzimidazole series.

---

Organizational Affiliation: 

Medicinal Chemistry, Amgen Inc., 360 Binney St., Cambridge, MA 02142, 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: 110.52 kDa 
• Atom Count: 6,556 
• Modelled Residue Count: 819 
• 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
0TZ	F [auth A]	3-(4-amino-6-methyl-1,3,5-triazin-2-yl)-N-(1H-pyrazol-5-yl)imidazo[1,2-a]pyridin-2-amine C14 H13 N9 OEQWYIZFUDGMEW-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.442	α = 90
b = 67.3	β = 95.67
c = 106.039	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Shaffer, P.L., Tang, J., Yakowec, P.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description