2O5K | pdb_00002o5k

Crystal Structure of GSK3beta in complex with a benzoimidazol inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2O5K/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-12-06 Released: 2007-10-23 
• Deposition Author(s): Shin, D., Lee, S.C., Heo, Y.S., Cho, Y.S., Kim, Y.E., Hyun, Y.L., Cho, J.M., Lee, Y.S., Ro, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.309 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

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

• PubMed: 17764934 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.78 kDa 
• Atom Count: 2,824 
• Modeled Residue Count: 350 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A	372	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBM	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
ID	Source	Binding Affinity
HBM	BindingDB:  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 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.94	α = 90
b = 72.632	β = 90
c = 81.795	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Shin, D., Lee, S.C., Heo, Y.S., Cho, Y.S., Kim, Y.E., Hyun, Y.L., Cho, J.M., Lee, Y.S., Ro, S.

Revision History  

• 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