3M1S

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.134 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1007/s00775-010-0699-x

  • 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 compar ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase kinase-3 beta
A, B
420Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DW1
Query on DW1

Download SDF File 
Download CCD File 
A, B
Ruthenium pyridocarbazole
C23 H13 N3 O4 Ru
KERGYDCAYYYADM-LLJXBBMBCD
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DW1IC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.134 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 83.041α = 90.00
b = 86.114β = 90.00
c = 177.398γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
PHENIXrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-26
    Type: Database references