2O5K

Crystal Structure of GSK3beta in complex with a benzoimidazol inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and synthesis of 7-hydroxy-1H-benzoimidazole derivatives as novel inhibitors of glycogen synthase kinase-3beta

Shin, D.Lee, S.C.Heo, Y.S.Lee, W.Y.Cho, Y.S.Kim, Y.E.Hyun, Y.L.Cho, J.M.Lee, Y.S.Ro, S.

(2007) Bioorg Med Chem Lett 17: 5686-5689

  • DOI: https://doi.org/10.1016/j.bmcl.2007.07.056
  • Primary Citation of Related Structures:  
    2O5K

  • PubMed Abstract: 

    A hydroxy functional group was introduced as the hydrogen bond donor and acceptor at the hinge region of protein kinase in order to develop novel ATP-competitive inhibitors. Several derivatives of 7-hydroxyl-1H-benzoimidazole were designed as inhibitors of glycogen synthase kinase-3beta with the help of ab initio calculations and a docking study. Enzymatic assay and an X-ray complex study showed that these designed compounds were highly potent ATP-competitive inhibitors.


  • Organizational Affiliation

    CrystalGenomics, Inc., Asan Institute for Life Sciences, 388-1 Pungnap-2dong, Songpa-gu, Seoul 138-736, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta372Homo sapiensMutation(s): 0 
EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (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
HBM
Query on HBM

Download Ideal Coordinates CCD File 
B [auth A]2-(2,4-DICHLORO-PHENYL)-7-HYDROXY-1H-BENZOIMIDAZOLE-4-CARBOXYLIC ACID [2-(4-METHANESULFONYLAMINO-PHENYL)-ETHYL]-AMIDE
C23 H20 Cl2 N4 O4 S
BFHQTAMNYUCFBP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
HBM BindingDB:  2O5K IC50: 15 (nM) from 1 assay(s)
PDBBind:  2O5K IC50: 15 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.94α = 90
b = 72.632β = 90
c = 81.795γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description