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 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
A, B, C
382Homo sapiensMutation(s): 0 
Gene Names: DYRK1A (DYRK, MNB, MNBH)
EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens)
Go to Gene View: DYRK1A
Go to UniProtKB:  Q13627
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
E, F, G
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3RA
Query on 3RA

Download SDF File 
Download 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  3 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, E, F, G
L-PEPTIDE LINKINGC3 H8 N O6 PSER
UNK
Query on UNK
E, F, G
L-PEPTIDE LINKINGC4 H9 N O2

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PTR
Query on PTR
A, B, C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3RAKd: 7.8 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 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 111.649α = 90.00
b = 111.649β = 90.00
c = 301.725γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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