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), 0.213 (DCC) 
  • R-Value Work: 
    0.208 (Depositor) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 99.31 kDa 
  • Atom Count: 5,500 
  • Modeled Residue Count: 679 
  • 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.222 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.208 (Depositor) 
  • 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 


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