Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.07 kDa 
• Atom Count: 2486 
• Modelled Residue Count: 274 
• Deposited Residue Count: 293 
• Unique protein chains: 1

5AUZ

Crystal structure of DAPK1 in complex with genistein.

• PDB DOI: 10.2210/pdb5AUZ/pdb

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


• Deposited: 2015-06-10 Released: 2015-10-07 
• Deposition Author(s): Yokoyama, T., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.206 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

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

• PubMed: 26322379 
• DOI: 10.1021/acs.jmedchem.5b00893
• Primary Citation of Related Structures:  
  5AUT, 5AUU, 5AUV, 5AUW, 5AUX, 5AUY, 5AUZ, 5AV0, 5AV1, 5AV2, 5AV3, 5AV4


• 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 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.

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Organizational Affiliation: 

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GEN	B [auth A]	GENISTEIN C15 H10 O5 TZBJGXHYKVUXJN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GEN	Binding MOAD:  5AUZ	IC50: 9.80e+4 (nM) from 1 assay(s)
	BindingDB:  5AUZ	IC50: 9.80e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.206 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.72	α = 90
b = 62.318	β = 90
c = 88.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-06-10 
• Released Date: 2015-10-07 
Deposition Author(s): Yokoyama, T., Mizuguchi, M.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary