4TXC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death-associated protein kinase 1
A
304Homo 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
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
38G
Query on 38G

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
38GKd: 240 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.951 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.900α = 90.00
b = 77.290β = 90.00
c = 110.120γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-11-19
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary