1Q5K | pdb_00001q5k

crystal structure of Glycogen synthase kinase 3 in complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.242 (Depositor) 
  • R-Value Work: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1Q5K

This is version 1.3 of the entry. See complete history

Literature

Structural insights and biological effects of glycogen synthase kinase 3-specific inhibitor AR-A014418.

Bhat, R.Xue, Y.Berg, S.Hellberg, S.Ormo, M.Nilsson, Y.Radesater, A.C.Jerning, E.Markgren, P.O.Borgegard, T.Nylof, M.Gimenez-Cassina, A.Hernandez, F.Lucas, J.J.Diaz-Nido, J.Avila, J.

(2003) J Biological Chem 278: 45937-45945

  • DOI: https://doi.org/10.1074/jbc.M306268200
  • Primary Citation Related Structures: 
    1Q5K

  • PubMed Abstract: 

    Glycogen synthase kinase 3 (GSK3) is a serine/threonine kinase that has been implicated in pathological conditions such as diabetes and Alzheimer's disease. We report the characterization of a GSK3 inhibitor, AR-A014418, which inhibits GSK3 (IC50 = 104 +/- 27 nM), in an ATP-competitive manner (Ki = 38 nM). AR-A014418 does not significantly inhibit cdk2 or cdk5 (IC50 > 100 microM) or 26 other kinases demonstrating high specificity for GSK3. We report the co-crystallization of AR-A014418 with the GSK3beta protein and provide a description of the interactions within the ATP pocket, as well as an understanding of the structural basis for the selectivity of AR-A014418. AR-A014418 inhibits tau phosphorylation at a GSK3-specific site (Ser-396) in cells stably expressing human four-repeat tau protein. AR-A014418 protects N2A neuroblastoma cells against cell death mediated by inhibition of the phosphatidylinositol 3-kinase/protein kinase B survival pathway. Furthermore, AR-A014418 inhibits neurodegeneration mediated by beta-amyloid peptide in hippocampal slices. AR-A014418 may thus have important applications as a tool to elucidate the role of GSK3 in cellular signaling and possibly in Alzheimer's disease. AR-A014418 is the first compound of a family of specific inhibitors of GSK3 that does not significantly inhibit closely related kinases such as cdk2 or cdk5.


  • Organizational Affiliation
    • AstraZeneca R&D, 15185 Södertälje, Sweden, AstraZeneca R&D, 43183 Mölndal, Sweden. ratan.bhat@astrazeneca.com

Macromolecule Content 

  • Total Structure Weight: 92.85 kDa 
  • Atom Count: 5,930 
  • Modeled Residue Count: 689 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
414Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt), 2.7.11.26 (UniProt)
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
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TMU

Query on TMU



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
N-(4-METHOXYBENZYL)-N'-(5-NITRO-1,3-THIAZOL-2-YL)UREA
C12 H12 N4 O4 S
YAEMHJKFIIIULI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TMU BindingDB:  1Q5K Ki: min: 38, max: 770 (nM) from 2 assay(s)
IC50: min: 42, max: 3.30e+5 (nM) from 10 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.242 (Depositor) 
  • R-Value Work:  0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.584α = 90
b = 84.913β = 90
c = 178.424γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations