4AZE

Human DYRK1A in complex with Leucettine L41

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Selectivity, Co-Crystal Structures and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.

Tahtouh, T., Elkins, J.M., Filippakopoulos, P., Soundararajan, M., Burgy, G., Durieu, E., Cochet, C., Schmid, R.S., Lo, D.C., Delhommel, F., Oberholzer, A., Laurence, P., Carreaux, F., Bazureau, J.P., Knapp, S., Meijer, L.

(2012) J Med Chem 55: 9312

  • DOI: 10.1021/jm301034u
  • Primary Citation of Related Structures:  
    4B7T, 4AZE, 4AZF, 4GW8

  • PubMed Abstract: 

    • DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases) are implicated in the onset and development of Alzheimer's disease and Down syndrome. The marine sponge alkaloid leucettamine B was recently identified ...

    DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases) are implicated in the onset and development of Alzheimer's disease and Down syndrome. The marine sponge alkaloid leucettamine B was recently identified as an inhibitor of DYRKs/CLKs. Synthesis of analogues (leucettines) led to an optimized product, leucettine L41. Leucettines were cocrystallized with DYRK1A, DYRK2, CLK3, PIM1, and GSK-3β. The selectivity of L41 was studied by activity and interaction assays of recombinant kinases and affinity chromatography and competition affinity assays. These approaches revealed unexpected potential secondary targets such as CK2, SLK, and the lipid kinase PIKfyve/Vac14/Fig4. L41 displayed neuroprotective effects on glutamate-induced HT22 cell death. L41 also reduced amyloid precursor protein-induced cell death in cultured rat brain slices. The unusual multitarget selectivity of leucettines may account for their neuroprotective effects. This family of kinase inhibitors deserves further optimization as potential therapeutics against neurodegenerative diseases such as Alzheimer's disease.

    Organizational Affiliation: 

    CNRS, "Protein Phosphorylation & Human Disease" Group, Station Biologique, 29680 Roscoff, Bretagne, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1AA, B, C382Homo sapiensMutation(s): 0 
Gene Names: DYRK1A, DYRK, MNB, MNBH
EC: 2.7.12.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
NIH Common Fund Data Resources
PHAROS  Q13627
GTEx  ENSG00000157540
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1AE, F, G4Homo sapiensMutation(s): 0 
EC: 2.7.12.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3RA
Query on 3RA
Download Ideal Coordinates CCD File 
A, B, C
5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one
C17 H13 N3 O3
ZDINVWCJHPMIKS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR		A,B,CL-PEPTIDE LINKINGC9 H12 N O6 PTYR
SEP
Query on SEP		A,B,CL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3RAKd :  7.800000190734863   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.649α = 90
b = 111.649β = 90
c = 301.725γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references, Derived calculations
  • Version 1.2: 2012-11-21
    Changes: Database references