3M1S | pdb_00003m1s

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

• PDB DOI: https://doi.org/10.2210/pdb3M1S/pdb

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


• Deposited: 2010-03-05 Released: 2010-12-22 
• Deposition Author(s): Atilla-Gokcumen, G.E., Di Costanzo, L., Zimmermann, G., Meggers, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.228 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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

• PubMed: 20821241 
• DOI: https://doi.org/10.1007/s00775-010-0699-x
• Primary Citation Related Structures: 
  3M1S


• 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.6 kDa 
• Atom Count: 5,579 
• Modeled Residue Count: 697 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	420	Homo sapiens	Mutation(s): 0  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
DW1	C [auth A], D [auth B]	Ruthenium pyridocarbazole C23 H13 N3 O4 Ru KERGYDCAYYYADM-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.228 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.041	α = 90
b = 86.114	β = 90
c = 177.398	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Atilla-Gokcumen, G.E., Di Costanzo, L., Zimmermann, G., Meggers, E.

Revision History  

• 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