5A6N

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with compound 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.2 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:  
    5A6N, 5A6O

  • 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. 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 ...

    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). gisbert.schneider@pharma.ethz.ch.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEATH-ASSOCIATED PROTEIN KINASE 3A, B283Homo sapiensMutation(s): 0 
Gene Names: DAPK3, ZIPK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43293 (Homo sapiens)
Explore O43293 
Go to UniProtKB:  O43293
PHAROS:  O43293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43293
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U7E
Query on U7E
Download Ideal Coordinates CCD File 
C [auth A]5-(3-SULFAMOYLPHENYL)-1H-1,2,3,4-TETRAZOL-1-IDE
C7 H7 N5 O2 S
BIOBAIFFWOWFPU-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
PGO
Query on PGO
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
U7E Binding MOAD:  5A6N IC50: 5.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.726α = 90
b = 87.775β = 90
c = 91.301γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2016-01-27
    Changes: Database references