5AUV

Crystal structure of DAPK1 in complex with apigenin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Insight into the Interactions between Death-Associated Protein Kinase 1 and Natural Flavonoids.

Yokoyama, T.Kosaka, Y.Mizuguchi, M.

(2015) J.Med.Chem. 58: 7400-7408

  • DOI: 10.1021/acs.jmedchem.5b00893
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Death-associated protein kinase 1 (DAPK1) is a 160 kDa serine/threonine protein kinase that belongs to the Ca(2+)/calmodulin-dependent protein kinase subfamily. DAPK1 is a possible target for the treatment of acute ischemic stroke and endometrial ade ...

    Death-associated protein kinase 1 (DAPK1) is a 160 kDa serine/threonine protein kinase that belongs to the Ca(2+)/calmodulin-dependent protein kinase subfamily. DAPK1 is a possible target for the treatment of acute ischemic stroke and endometrial adenocarcinomas. In the present study, we investigated the binding characteristics of 17 natural flavonoids to DAPK1 using a 1-anilinonaphthalene-8-sulfonic acid competitive binding assay and revealed that morin was the strongest binder among the selected compounds. The crystallographic analysis of DAPK1 and 7 selected flavonoid complexes revealed the structure-binding affinity relationship in atomic-level detail. It was suggested that the high affinity of morin could be accounted for by the ionic interaction between 2'-OH and K42 and that such an interaction would not take place with either cyclin-dependent protein kinases or PIM kinases because of their broader entrance regions. Thus, morin would be a more selective inhibitor of DAPK1 than either of these other types of kinases. In addition, we found that the binding of kaempferol to DAPK1 was associated with a chloride ion. The present study provides a better understanding of the molecular properties of the ATP site of DAPK1 and may be useful for the design of specific DAPK1 inhibitors.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama , 2630 Sugitani, Toyama 930-0914, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death-associated protein kinase 1
A
293Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGI
Query on AGI

Download SDF File 
Download CCD File 
A
5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one
Apigenin
C15 H10 O5
KZNIFHPLKGYRTM-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AGIIC50: 31000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.884α = 90.00
b = 62.227β = 90.00
c = 88.446γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release