7OY6 | pdb_00007oy6

Crystal structure of human DYRK1A in complex with ARN25068


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 
    0.270 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

ARN25068, a versatile starting point towards triple GSK-3 beta /FYN/DYRK1A inhibitors to tackle tau-related neurological disorders.

Demuro, S.Sauvey, C.Tripathi, S.K.Di Martino, R.M.C.Shi, D.Ortega, J.A.Russo, D.Balboni, B.Giabbai, B.Storici, P.Girotto, S.Abagyan, R.Cavalli, A.

(2022) Eur J Med Chem 229: 114054-114054

  • DOI: https://doi.org/10.1016/j.ejmech.2021.114054
  • Primary Citation Related Structures: 
    7OY5, 7OY6

  • PubMed Abstract: 

    The human kinome plays a crucial role in several pathways. Its dysregulation has been linked to diverse central nervous system (CNS)-related disorders with a drastic impact on the aging population. Among them, tauopathies, such as Alzheimer's Disease (AD) and Frontotemporal Lobar degeneration (FTLD-tau), are neurodegenerative disorders pathologically defined by the presence of hyperphosphorylated tau-positive intracellular inclusions known as neurofibrillary tangles (NFTs). Compelling evidence has reported the great potential of the simultaneous modulation of multiple protein kinases (PKs) involved in abnormal tau phosphorylation through a concerted pharmacological approach to achieve a superior therapeutic effect relative to classic "one target, one drug" approaches. Here, we report on the identification and characterization of ARN25068 (4), a low nanomolar and well-balanced dual GSK-3β and FYN inhibitor, which also shows inhibitory activity against DYRK1A, an emerging target in AD and tauopathies. Computational and X-Ray studies highlight compound 4's typical H-bonding pattern of ATP-competitive inhibitors at the binding sites of all three PKs. In a tau phosphorylation assay on Tau0N4R-TM-tGFP U2OS cell line, 4 reduces the extent of tau phosphorylation, promoting tau-stabilized microtubule bundles. In conclusion, this compound emerges as a promising prototype for further SAR explorations to develop potent and well-balanced triple GSK-3β/FYN/DYRK1A inhibitors to tackle tau hyperphosphorylation.


  • Organizational Affiliation
    • Computational and Chemical Biology, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy; Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.

Macromolecule Content 

  • Total Structure Weight: 42.23 kDa 
  • Atom Count: 2,798 
  • Modeled Residue Count: 343 
  • Deposited Residue Count: 359 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 1AA [auth C]359Homo sapiensMutation(s): 0 
Gene Names: DYRK1ADYRKMNBMNBH
EC: 2.7.12.1 (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

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
39I
(Subject of Investigation/LOI)

Query on 39I



Download:Ideal Coordinates CCD File
B [auth C]~{N}4-(3-cyclopropyl-1~{H}-pyrazol-5-yl)-~{N}2-(phenylmethyl)thieno[3,2-d]pyrimidine-2,4-diamine
C19 H18 N6 S
TVUWQDLBEOZVOU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A [auth C]L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free:  0.270 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.65α = 90
b = 93.65β = 90
c = 48.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary