5A6O

Crystal structure of the apo form of the unphosphorylated human death associated protein kinase 3 (DAPK3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

De Novo Fragment Design for Drug Discovery and Chemical Biology.

Rodrigues, T.Reker, D.Welin, M.Caldera, M.Brunner, C.Gabernet, G.Schneider, P.Walse, B.Schneider, G.

(2015) Angew.Chem.Int.Ed.Engl. 54: 15079

  • DOI: 10.1002/anie.201508055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Automated molecular de novo design led to the discovery of an innovative inhibitor of death-associated protein kinase 3 (DAPK3). An unprecedented crystal structure of the inactive DAPK3 homodimer shows the fragment-like hit bound to the ATP pocket. T ...

    Automated molecular de novo design led to the discovery of an innovative inhibitor of death-associated protein kinase 3 (DAPK3). An unprecedented crystal structure of the inactive DAPK3 homodimer shows the fragment-like hit bound to the ATP pocket. Target prediction software based on machine learning models correctly identified additional macromolecular targets of the computationally designed compound and the structurally related marketed drug azosemide. The study validates computational de novo design as a prime method for generating chemical probes and starting points for drug discovery.


    Organizational Affiliation

    Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEATH-ASSOCIATED PROTEIN KINASE 3
A, B
283Homo sapiensMutation(s): 0 
Gene Names: DAPK3 (ZIPK)
EC: 2.7.11.1
Find proteins for O43293 (Homo sapiens)
Go to Gene View: DAPK3
Go to UniProtKB:  O43293
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download SDF File 
Download CCD File 
A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.569α = 90.00
b = 87.465β = 90.00
c = 90.711γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references
  • Version 1.2: 2016-01-27
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Data collection