8DJD | pdb_00008djd

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: 2.21 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted U3EClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structure-activity relationship (SAR) studies on substituted N-(pyridin-3-yl)-2-amino-isonicotinamides as highly potent and selective glycogen synthase kinase-3 (GSK-3) inhibitors.

Luo, G.Chen, L.Jacutin-Porte, S.Han, Y.Burton, C.R.Xiao, H.Krause, C.M.Cao, Y.Liu, N.Kish, K.Lewis, H.A.Macor, J.E.Dubowchik, G.M.

(2023) Bioorg Med Chem Lett 81: 129143-129143

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129143
  • Primary Citation of Related Structures:  
    8DJD

  • PubMed Abstract: 

    In our continuing efforts to explore structure-activity relationships around the novel class of potent, isonicotinamide-based GSK3 inhibitors described in our previous report, we extensively explored structural variations around both 4/5-pyridine substitutions and the amide group. Some analogs were found to have greatly improved pTau lowering potency while retaining high kinase selectivity. In contrast to previous active compounds 1a-c, a close analog 3h did not show in vivo efficacy in a triple-transgenic mouse Alzheimer's disease model. In general, these 2‑pyridinyl amide derivatives were prone to amidase mediated hydrolysis in mouse plasma.


  • Organizational Affiliation

    Bristol-Myers Squibb, Wallingford, CT 06492, United States; Bristol Myers Squibb, Lawrenceville, NJ 08543, United States. Electronic address: guanglin.luo@bms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Binding Affinity Annotations 
IDSourceBinding Affinity
U3E BindingDB:  8DJD IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.677α = 90
b = 83.659β = 90
c = 177.306γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted U3EClick on this verticalbar to view details

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: 2024-04-03
    Changes: Data collection, Refinement description