6DGT | pdb_00006dgt

Selective PI3K beta inhibitor bound to PI3K delta

• PDB DOI: https://doi.org/10.2210/pdb6DGT/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-18 Released: 2018-08-01 
• Deposition Author(s): Somoza, J., Villasenor, A., McGrath, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.318 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.231 (Depositor) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Atropisomerism by Design: Discovery of a Selective and Stable Phosphoinositide 3-Kinase (PI3K) beta Inhibitor.

Chandrasekhar, J., Dick, R., Van Veldhuizen, J., Koditek, D., Lepist, E.I., McGrath, M.E., Patel, L., Phillips, G., Sedillo, K., Somoza, J.R., Therrien, J., Till, N.A., Treiberg, J., Villasenor, A.G., Zherebina, Y., Perreault, S.

(2018) J Med Chem 61: 6858-6868

• PubMed: 30015489 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b00797
• Primary Citation Related Structures: 
  6DGT


• PubMed Abstract: 
  

  Atropisomerism is a type of axial chirality in which enantiomers or diastereoisomers arise due to hindered rotation around a bond axis. In this manuscript, we report a case in which torsional scan studies guided the thoughtful creation of a restricted axis of rotation between two heteroaromatic systems of a phosphoinositide 3-kinase (PI3K) β inhibitor, generating a pair of atropisomeric compounds with significantly different pharmacological and pharmacokinetic profiles. Emblematic of these differences, the metabolism of inactive ( M)-28 is primarily due to the cytosolic enzyme aldehyde oxidase, while active ( P)-28 has lower affinity for aldehyde oxidase, resulting in substantially better metabolic stability. Additionally, we report torsional scan and experimental studies used to determine the barriers of rotation of this novel PI3Kβ inhibitor.

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Organizational Affiliation: 
• Gilead Sciences, Inc. , 199 East Blaine Street , Seattle , Washington 98102 , United States.
Gilead Sciences, Inc. , 333 Lakeside Drive , Foster City , California 94404 , United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 108.11 kDa 
• Atom Count: 6,296 
• Modeled Residue Count: 777 
• Deposited Residue Count: 938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	938	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GFJ	B [auth A]	4-[1-(5,8-difluoroquinolin-4-yl)-2-methyl-4-(4H-1,2,4-triazol-3-yl)-1H-benzimidazol-6-yl]-3-fluoropyridin-2-amine C24 H15 F3 N8 SBVBUGSOYHJGGD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.318 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.231 (Depositor) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.517	α = 90
b = 143.502	β = 90
c = 221.256	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Somoza, J., Villasenor, A., McGrath, M.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2018-08-22
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references