8DJE | pdb_00008dje

CRYSTAL STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 3-[(CYCLOPROPYLMETHYL)AMINO] -N-(4-PHENYLPYRIDIN-3-YL)IMIDAZO[1,2-B]PYRIDAZINE-8-CARBOX AMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.227 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design, Structure-Activity Relationships, and In Vivo Evaluation of Potent and Brain-Penetrant Imidazo[1,2- b ]pyridazines as Glycogen Synthase Kinase-3 beta (GSK-3 beta ) Inhibitors.

Hartz, R.A.Ahuja, V.T.Sivaprakasam, P.Xiao, H.Krause, C.M.Clarke, W.J.Kish, K.Lewis, H.Szapiel, N.Ravirala, R.Mutalik, S.Nakmode, D.Shah, D.Burton, C.R.Macor, J.E.Dubowchik, G.M.

(2023) J Med Chem 66: 4231-4252

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00133
  • Primary Citation Related Structures: 
    8DJC, 8DJE

  • PubMed Abstract: 

    Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase that regulates numerous cellular processes, including metabolism, proliferation, and cell survival. Due to its multifaceted role, GSK-3 has been implicated in a variety of diseases, including Alzheimer's disease, type 2 diabetes, cancer, and mood disorders. GSK-3β has been linked to the formation of the neurofibrillary tangles associated with Alzheimer's disease that arise from the hyperphosphorylation of tau protein. The design and synthesis of a series of imidazo[1,2- b ]pyridazine derivatives that were evaluated as GSK-3β inhibitors are described herein. Structure-activity relationship studies led to the identification of potent GSK-3β inhibitors. In vivo studies with 47 in a triple-transgenic mouse Alzheimer's disease model showed that this compound is a brain-penetrant, orally bioavailable GSK-3β inhibitor that significantly lowered levels of phosphorylated tau.


  • Organizational Affiliation
    • Biocon-Bristol Myers Squibb Research and Development Center, Biocon Park, Plot No. 2 & 3, Bommasandra Phase IV, Jigani Link Road, Bangalore 560099, India.

Macromolecule Content 

  • Total Structure Weight: 99.36 kDa 
  • Atom Count: 5,558 
  • Modeled Residue Count: 690 
  • Deposited Residue Count: 882 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
441Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens)
Explore P49841 
Go to UniProtKB:  P49841
PHAROS:  P49841
GTEx:  ENSG00000082701 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49841
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6S
(Subject of Investigation/LOI)

Query on U6S



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(4S)-3-[(cyclopropylmethyl)amino]-N-(4-phenylpyridin-3-yl)imidazo[1,2-b]pyridazine-8-carboxamide
C22 H20 N6 O
UXFHOMCAQUWAHI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.227 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.144α = 90
b = 83.763β = 90
c = 176.952γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection