2OW3 | pdb_00002ow3

Glycogen synthase kinase-3 beta in complex with bis-(indole)maleimide pyridinophane inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2OW3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2007-02-15 Released: 2008-02-19 
• Deposition Author(s): Zhang, H.C., Bonaga, L.V., Ye, H., Derian, C.K., Damiano, B.P., Maryanoff, B.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.295 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Novel bis(indolyl)maleimide pyridinophanes that are potent, selective inhibitors of glycogen synthase kinase-3.

Zhang, H.C., Bonaga, L.V., Ye, H., Derian, C.K., Damiano, B.P., Maryanoff, B.E.

(2007) Bioorg Med Chem Lett 17: 2863-2868

• PubMed: 17350261 
• DOI: https://doi.org/10.1016/j.bmcl.2007.02.059
• Primary Citation Related Structures: 
  2OW3


• PubMed Abstract: 
  

  Novel bis(indolyl)maleimide pyridinophanes 3, 9a, 9b, 10a, 10b, and 11 were prepared by cobalt-mediated [2+2+2] cycloaddition of an appropriate alpha,omega-diyne with an N,N-dialkylcyanamide. These macrocyclic heterophanes were found to be potent, selective inhibitors of glycogen synthase kinase-3beta. An X-ray structure of a co-crystal of GSK-3beta and 3 (IC(50)=3nM) depicts the hydrogen bonding and hydrophobic interactions in the ATP-binding pocket of this serine/threonine protein kinase.

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Organizational Affiliation: 
• Vascular Research Team, Johnson & Johnson Pharmaceutical Research & Development, Spring House, PA 19477-0776, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.25 kDa 
• Atom Count: 5,681 
• Modeled Residue Count: 699 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	352	Homo sapiens	Mutation(s): 1  Gene Names: GSK3B 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
BIM	C [auth A], D [auth B]	BIS-(INDOLE)MALEIMIDE PYRIDINOPHANE C34 H33 N5 O2 WHEOASILVTUPNR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
BIM	BindingDB:  2OW3	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.295 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.472	α = 90
b = 117.329	β = 103.22
c = 69.461	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-19 
Deposition Author(s): Zhang, H.C., Bonaga, L.V., Ye, H., Derian, C.K., Damiano, B.P., Maryanoff, B.E.

Revision History  

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-11-13
  Changes: Structure summary