5A6O

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

• PDB DOI: https://doi.org/10.2210/pdb5A6O/pdb

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


• Deposited: 2015-06-30 Released: 2015-10-21 
• Deposition Author(s): Rodrigues, T., Reker, D., Welin, M., Caldera, M., Brunner, C., Gabernet, G., Schneider, P., Walse, B., Schneider, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.225 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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

• PubMed: 26486226 
• DOI: https://doi.org/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. 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).

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 65.52 kDa 
• Atom Count: 4,689 
• Modelled Residue Count: 531 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEATH-ASSOCIATED PROTEIN KINASE 3	A, B	283	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000167657

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
PGO	E [auth A], G [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.225 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.569	α = 90
b = 87.465	β = 90
c = 90.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Rodrigues, T., Reker, D., Welin, M., Caldera, M., Brunner, C., Gabernet, G., Schneider, P., Walse, B., Schneider, G.

Revision History  

• 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
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description