3PUP

Structure of Glycogen Synthase Kinase 3 beta (GSK3B) in complex with a ruthenium octasporine ligand (OS1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structurally sophisticated octahedral metal complexes as highly selective protein kinase inhibitors.

Feng, L.Geisselbrecht, Y.Blanck, S.Wilbuer, A.Atilla-Gokcumen, G.E.Filippakopoulos, P.Kraling, K.Celik, M.A.Harms, K.Maksimoska, J.Marmorstein, R.Frenking, G.Knapp, S.Essen, L.O.Meggers, E.

(2011) J Am Chem Soc 133: 5976-5986

  • DOI: 10.1021/ja1112996
  • Primary Citation of Related Structures:  
    2YAK, 3PUP

  • PubMed Abstract: 
  • The generation of synthetic compounds with exclusive target specificity is an extraordinary challenge of molecular recognition and demands novel design strategies, in particular for large and homologous protein families such as protein kinases with more than 500 members ...

    The generation of synthetic compounds with exclusive target specificity is an extraordinary challenge of molecular recognition and demands novel design strategies, in particular for large and homologous protein families such as protein kinases with more than 500 members. Simple organic molecules often do not reach the necessary sophistication to fulfill this task. Here, we present six carefully tailored, stable metal-containing compounds in which unique and defined molecular geometries with natural-product-like structural complexity are constructed around octahedral ruthenium(II) or iridium(III) metal centers. Each of the six reported metal compounds displays high selectivity for an individual protein kinase, namely GSK3α, PAK1, PIM1, DAPK1, MLCK, and FLT4. Although being conventional ATP-competitive inhibitors, the combination of the unusual globular shape and rigidity characteristics, of these compounds facilitates the design of highly selective protein kinase inhibitors. Unique structural features of the octahedral coordination geometry allow novel interactions with the glycine-rich loop, which contribute significantly to binding potencies and selectivities. The sensitive correlation between metal coordination sphere and inhibition properties suggests that in this design, the metal is located at a "hot spot" within the ATP binding pocket, not too close to the hinge region where globular space is unavailable, and at the same time not too far out toward the solvent where the octahedral coordination sphere would not have a significant impact on potency and selectivity. This study thus demonstrates that inert (stable) octahedral metal complexes are sophisticated structural scaffolds for the design of highly selective chemical probes.


    Related Citations: 
    • Targeting large kinase active site with rigid, bulky octahedral ruthenium complexes.
      Maksimoska, J., Feng, L., Harms, K., Yi, C., Kissil, J., Marmorstein, R., Meggers, E.
      (2008) J Am Chem Soc 130: 15764
    • Extremely tight binding of a ruthenium complex to glycogen synthase kinase 3.
      Atilla-Gokcumen, G.E., Pagano, N., Streu, C., Maksimoska, J., Filippakopoulos, P., Knapp, S., Meggers, E.
      (2008) Chembiochem 9: 2933

    Organizational Affiliation

    Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen synthase kinase-3 betaA, B420Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS1
Query on OS1

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]Ruthenium octasporine
C24 H16 Cl N6 O3 Ru
QQATVYHLKPGOMG-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OS1IC50 :  6   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.32α = 90
b = 84.3β = 90
c = 178.12γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



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: 2012-02-29
    Changes: Database references