6TCU | pdb_00006tcu

Glycogen synthase kinase-3 beta (GSK3b) in complex with ligand 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.240 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Optimization of Indazole-Based GSK-3 Inhibitors with Mitigated hERG Issue andIn VivoActivity in a Mood Disorder Model.

Prati, F.Buonfiglio, R.Furlotti, G.Cavarischia, C.Mangano, G.Picollo, R.Oggianu, L.di Matteo, A.Olivieri, S.Bovi, G.Porceddu, P.F.Reggiani, A.Garrone, B.Di Giorgio, F.P.Ombrato, R.

(2020) ACS Med Chem Lett 11: 825-831

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00633
  • Primary Citation Related Structures: 
    6TCU

  • PubMed Abstract: 

    Bipolar disorders still represent a global unmet medical need and pose a requirement for novel effective treatments. In this respect, glycogen synthase kinase 3β (GSK-3β) aberrant activity has been linked to the pathophysiology of several disease conditions, including mood disorders. Therefore, the development of GSK-3β inhibitors with good in vivo efficacy and safety profile associated with high brain exposure is required. Accordingly, we have previously reported the selective indazole-based GSK-3 inhibitor 1 , which showed excellent efficacy in a mouse model of mania. Despite the favorable preclinical profile, analog 1 suffered from activity at the hERG ion channel, which prevented its further progression. Herein, we describe our strategy to improve this off-target liability through modulation of physicochemical properties, such as lipophilicity and basicity. These efforts led to the potent inhibitor 14 , which possessed reduced hERG affinity, promising in vitro ADME properties, and was very effective in a mood stabilizer in vivo model.


  • Organizational Affiliation
    • Angelini Pharma S.p.A., Viale Amelia, 70, 00181 Rome, Italy.

Macromolecule Content 

  • Total Structure Weight: 40.89 kDa 
  • Atom Count: 2,940 
  • Modeled Residue Count: 350 
  • Deposited Residue Count: 355 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta355Homo 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

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.240 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.783α = 90
b = 107.851β = 90
c = 104.226γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Advisory, Data collection, Database references, Structure summary