9INV

Crystal structure of DAPK1 in complex with isoliquiritigenin

• PDB DOI: https://doi.org/10.2210/pdb9INV/pdb

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


• Deposited: 2024-07-08 Released: 2024-10-09 
• Deposition Author(s): Yokoyama, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Starting Model: experimental

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

• PubMed: 39243455 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,468 
• Modelled Residue Count: 275 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	293	Homo sapiens	Mutation(s): 0  Gene Names: DAPK1, DAPK 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCC (Subject of Investigation/LOI)	B [auth A]	2',4,4'-TRIHYDROXYCHALCONE C15 H12 O4 DXDRHHKMWQZJHT-FPYGCLRLSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.205 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.623	α = 90
b = 62.279	β = 90
c = 88.654	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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