3F88

glycogen synthase Kinase 3beta inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design, synthesis and structure-activity relationships of 1,3,4-oxadiazole derivatives as novel inhibitors of glycogen synthase kinase-3beta.

Saitoh, M.Kunitomo, J.Kimura, E.Hayase, Y.Kobayashi, H.Uchiyama, N.Kawamoto, T.Tanaka, T.Mol, C.D.Dougan, D.R.Textor, G.S.Snell, G.P.Itoh, F.

(2009) Bioorg.Med.Chem. 17: 2017-2029

  • DOI: 10.1016/j.bmc.2009.01.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycogen synthase kinase-3beta (GSK-3beta) is implicated in abnormal hyperphosphorylation of tau protein and its inhibitors are expected to be a promising therapeutic agents for the treatment of Alzheimer's disease. Here we report design, synthesis a ...

    Glycogen synthase kinase-3beta (GSK-3beta) is implicated in abnormal hyperphosphorylation of tau protein and its inhibitors are expected to be a promising therapeutic agents for the treatment of Alzheimer's disease. Here we report design, synthesis and structure-activity relationships of a novel series of oxadiazole derivatives as GSK-3beta inhibitors. Among these inhibitors, compound 20x showed highly selective and potent GSK-3beta inhibitory activity in vitro and its binding mode was determined by obtaining the X-ray co-crystal structure of 20x and GSK-3beta.


    Organizational Affiliation

    Pharmaceutical Research Division, Medicinal Chemistry Research Laboratories, Takeda Pharmaceutical Company, Ltd, Osaka, Japan. Saitoh_Morihisa@takeda.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase kinase-3 beta
A, B
349Homo sapiensMutation(s): 0 
Gene Names: GSK3B
EC: 2.7.11.26
Find proteins for P49841 (Homo sapiens)
Go to Gene View: GSK3B
Go to UniProtKB:  P49841
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HT
Query on 3HT

Download SDF File 
Download CCD File 
A, B
5-[1-(4-methoxyphenyl)-1H-benzimidazol-6-yl]-1,3,4-oxadiazole-2(3H)-thione
C16 H12 N4 O2 S
QBVJMUOTMRYUKR-UHFFFAOYSA-N
 Ligand Interaction
2HT
Query on 2HT

Download SDF File 
Download CCD File 
A, B
3-methylbenzonitrile
C8 H7 N
BOHCMQZJWOGWTA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3HTIC50: 2.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.947α = 90.00
b = 111.785β = 100.84
c = 66.955γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description