9INX

Crystal structure of DAPK1 in complex with compound 10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Literature

Discovery and optimization of isoliquiritigenin as a death-associated protein kinase 1 inhibitor.

Yokoyama, T.Hisatomi, K.Oshima, S.Tanaka, I.Okada, T.Toyooka, N.

(2024) Eur J Med Chem 279: 116836-116836

  • DOI: https://doi.org/10.1016/j.ejmech.2024.116836
  • Primary Citation of Related Structures:  
    9INV, 9INW, 9INX

  • PubMed Abstract: 

    Death-associated protein kinase 1 (DAPK1) is a phosphotransferase in the serine/threonine kinase family. Inhibiting DAPK1 is expected to be beneficial in treating Alzheimer's disease and protecting neuronal cells during cerebral ischemia. In this study, we demonstrated that the natural chalcone isoliquiritigenin inhibits DAPK1 in an ATP-competitive manner, and we synthesized halogen derivatives to amplify the inhibitory effect. Among the compounds tested, the chlorine, bromine, and iodine derivatives exhibited high DAPK1 inhibitory activity and binding affinity. Crystal structure analysis revealed that this improvement is attributable to the halogen atoms fitting well into the hydrophobic pocket formed by I77, L93, and I160. In particular, the chlorine derivative showed a significant enthalpic contribution to the interaction with DAPK1, suggesting its potential as a primary compound for new DAPK1 inhibitors.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama, 930-0914, Japan. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Death-associated protein kinase 1293Homo sapiensMutation(s): 0 
Gene Names: DAPK1DAPK
EC: 2.7.11.1
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
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.603α = 90
b = 62.266β = 90
c = 88.397γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-10-09 
  • Deposition Author(s): Yokoyama, T.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release