8FF8 | pdb_00008ff8

CRYSTAL STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 BETA COMPLEXED WITH 2-[(4-CYANOPHENYL)AMINO]-N-(4-PHENYLPYRIDIN-3-YL)PYRIMIDINE-4-CARBOXAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 
    0.217 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of 2-(Anilino)pyrimidine-4-carboxamides as Highly Potent, Selective, and Orally Active Glycogen Synthase Kinase-3 (GSK-3) Inhibitors.

Hartz, R.A.Ahuja, V.T.Luo, G.Chen, L.Sivaprakasam, P.Xiao, H.Krause, C.M.Clarke, W.J.Xu, S.Tokarski, J.S.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: 7534-7552

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00364
  • Primary Citation Related Structures: 
    8FF8

  • PubMed Abstract: 

    Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase that serves as an important regulator of a broad range of cellular functions. It has been linked to Alzheimer's disease as well as various other diseases, including mood disorders, type 2 diabetes, and cancer. There is considerable evidence indicating that GSK-3β in the central nervous system plays a role in the production of abnormal, hyperphosphorylated, microtubule-associated tau protein found in neurofibrillary tangles associated with Alzheimer's disease. A series of analogues containing a pyrimidine-based hinge-binding heterocycle was synthesized and evaluated, leading to the identification of highly potent GSK-3 inhibitors with excellent kinase selectivity. Further evaluation of 34 and 40 in vivo demonstrated that these compounds are orally bioavailable, brain-penetrant GSK-3 inhibitors that lowered levels of phosphorylated tau in a triple-transgenic mouse Alzheimer's disease model.


  • 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: 99.37 kDa 
  • Atom Count: 5,622 
  • Modeled Residue Count: 693 
  • 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: 2.33 Å
  • R-Value Free:  0.217 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.843α = 90
b = 84.083β = 90
c = 177.788γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection