6DGT

Selective PI3K beta inhibitor bound to PI3K delta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acs.jmedchem.8b00797

  • 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 restricte ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
A
938Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153
Find proteins for O35904 (Mus musculus)
Go to UniProtKB:  O35904
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GFJ
Query on GFJ

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 63.517α = 90.00
b = 143.502β = 90.00
c = 221.256γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-08-22
    Type: Data collection, Database references