2YAK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 

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.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: 10.1021/ja1112996
  • Primary Citation of Related Structures:  

  • 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 m ...

    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 GSK3╬▒, 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-Universit├Ąt Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEATH-ASSOCIATED PROTEIN KINASE 1
A
285Homo sapiensMutation(s): 0 
Gene Names: DAPK1 (DAPK)
EC: 2.7.11.1
Find proteins for P53355 (Homo sapiens)
Go to Gene View: DAPK1
Go to UniProtKB:  P53355
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OSV
Query on OSV

Download SDF File 
Download CCD File 
A
RUTHENIUM OCTASPORINE 4
C27 H31 F N4 O3 Ru S4
ACWICPOFNPWEAE-CFZZCFLMSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OSVIC50: 2 nM BINDINGMOAD
OSVIC50: 2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.300α = 90.00
b = 77.800β = 90.00
c = 111.300γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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