4TXC | pdb_00004txc

Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4TXC/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-03 Released: 2014-07-23 
• Deposition Author(s): Sorrell, F.J., Krojer, T., Wilbek, T.S., Skovgaard, T., Berthelsen, J., Dixon-Clarke, S., Chalk, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Stromgaard, K., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Models: experimental

Literature

Identification and characterization of a small-molecule inhibitor of death-associated protein kinase 1.

Wilbek, T.S., Skovgaard, T., Sorrell, F.J., Knapp, S., Berthelsen, J., Strmgaard, K.

(2015) Chembiochem 16: 59-63

• PubMed: 25382253 
• DOI: https://doi.org/10.1002/cbic.201402512
• Primary Citation of Related Structures:  
  4TXC

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Organizational Affiliation: 
• Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen (Denmark).

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.57 kDa 
• Atom Count: 2,543 
• Modeled Residue Count: 276 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	304	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
38G	B [auth A]	4-(3-{3-[(R)-{[2-(dimethylamino)ethyl]amino}(hydroxy)methyl]phenyl}imidazo[1,2-b]pyridazin-6-yl)-2-methoxyphenol C24 H27 N5 O3 ASDVVHQAXNTHHM-XMMPIXPASA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.9	α = 90
b = 77.29	β = 90
c = 110.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Sorrell, F.J., Krojer, T., Wilbek, T.S., Skovgaard, T., Berthelsen, J., Dixon-Clarke, S., Chalk, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Stromgaard, K., Knapp, S.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2015-01-14
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description