7FHT image
Entry Detail
PDB ID:
7FHT
Keywords:
Title:
Crystal structure of DYRK1A in complex with RD0448
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-07-30
Release Date:
2022-03-23
Method Details:
Experimental Method:
Resolution:
2.68 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Chain IDs:A, B, C, D
Chain Length:361
Number of Molecules:4
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PTR A TYR modified residue
Ligand Molecules
Primary Citation
Structure-activity relationship for the folding intermediate-selective inhibition of DYRK1A.
Eur.J.Med.Chem. 227 113948 113948 (2022)
PMID: 34742017 DOI: 10.1016/j.ejmech.2021.113948

Abstact

DYRK1A phosphorylates proteins involved in neurological disorders in an intermolecular manner. Meanwhile, during the protein folding process of DYRK1A, a transitional folding intermediate catalyzes the intramolecular autophosphorylation required for the "one-off" inceptive activation and stabilization. In our previous study, a small molecule termed FINDY (1) was identified, which inhibits the folding intermediate-catalyzed intramolecular autophosphorylation of DYRK1A but not the folded state-catalyzed intermolecular phosphorylation. However, the structural features of FINDY (1) responsible for this intermediate-selective inhibition remain elusive. In this study, structural derivatives of FINDY (1) were designed and synthesized according to its predicted binding mode in the ATP pocket of DYRK1A. Quantitative structure-activity relationship (QSAR) of the derivatives revealed that the selectivity against the folding intermediate is determined by steric hindrance between the bulky hydrophobic moiety of the derivatives and the entrance to the pocket. In addition, a potent derivative 3 was identified, which inhibited the folding intermediate more strongly than FINDY (1); it was designated as dp-FINDY. Although dp-FINDY (3) did not inhibit the folded state, as well as FINDY (1), it inhibited the intramolecular autophosphorylation of DYRK1A in an in vitro cell-free protein synthesis assay. Furthermore, dp-FINDY (3) destabilized endogenous DYRK1A in HEK293 cells. This study provides structural insights into the folding intermediate-selective inhibition of DYRK1A and expands the chemical options for the design of a kinase inhibitor.

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Primary Citation of related structures