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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1021/jm301034u
  • Primary Citation of Related Structures:  
    4AZE, 4AZF, 4B7T, 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
A, B, C
382Homo sapiensMutation(s): 0 
EC: 2.7.12.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
PHAROS:  Q13627
GTEx:  ENSG00000157540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1AD [auth E],
E [auth F],
F [auth G]
4Homo sapiensMutation(s): 0 
EC: 2.7.12.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
SEP
Query on SEP
A, B, C
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
3RA PDBBind:  4AZE Kd: 7.8 (nM) from 1 assay(s)
BindingDB:  4AZE IC50: 7.6 (nM) from 1 assay(s)
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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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-09-08
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2023-12-20
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary