Structure of death-associated protein Kinase 1 (dapk1) in complex with a ruthenium octasporine ligand (OSV)

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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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.Kraeling, 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

  • DOI: https://doi.org/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. 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEATH-ASSOCIATED PROTEIN KINASE 1285Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens)
Explore P53355 
Go to UniProtKB:  P53355
PHAROS:  P53355
GTEx:  ENSG00000196730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53355
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on OSV

Download Ideal Coordinates CCD File 
C27 H31 F N4 O3 Ru S4
Binding Affinity Annotations 
IDSourceBinding Affinity
OSV PDBBind:  2YAK IC50: 2 (nM) from 1 assay(s)
Binding MOAD:  2YAK IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.3α = 90
b = 77.8β = 90
c = 111.3γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance