Structure of Ruthenium Half-Sandwich Complex Bound to Glycogen Synthase Kinase 3

Experimental Data Snapshot

  • Resolution: 3.13 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Structure of anticancer ruthenium half-sandwich complex bound to glycogen synthase kinase 3beta

Atilla-Gokcumen, G.E.Di Costanzo, L.Meggers, E.

(2011) J Biol Inorg Chem 16: 45-50

  • DOI: https://doi.org/10.1007/s00775-010-0699-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The 3.15-Å-resolution crystal structure of the R enantiomer of the highly bioactive and antiproliferative half-sandwich ruthenium complex DW12 bound to the ATP binding site of glycogen synthase kinase 3β (GSK-3β) is reported and the binding is compared with the GSK-3β binding of staurosporine and other organic inhibitors. The structure reveals a close packing of the organometallic inhibitor in the ATP binding site of GSK-3β via an induced-fit mechanism. The molecular structure of (R)-DW12 with the CO ligand oriented perpendicular to the pyridocarbazole heterocycle allows the complex to stretch the whole distance sandwiched between the faces of the N- and C-terminal lobes and to interact tightly with the flexible glycine-rich loop, which is uncommon for the interaction of GSK-3β with organic inhibitors.

  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 beta
A, B
420Homo sapiensMutation(s): 0 
Gene Names: GSK3B
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DW1 PDBBind:  3M1S IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.13 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.041α = 90
b = 86.114β = 90
c = 177.398γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-26
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description