9FT2 | pdb_00009ft2

Crystal structure of human DYRK1A in complex with ARN25699

• PDB DOI: https://doi.org/10.2210/pdb9FT2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2026-01-14 
• Deposition Author(s): Dalle Vedove, A., Demuro, S., Di Martino, R.M.C., Balboni, B., Tripathi, S.K., Storici, P., Girotto, S., Cavalli, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

A Polypharmacology-Driven Approach to Alzheimer's Disease and Tauopathies: Rational Design, Synthesis and Characterization of Amino-Pyrazole-Based Multikinase (GSK-3 beta /FYN-alpha /DYRK1A) Inhibitors.

Demuro, S., Russo, D., Penna, I., Grabska, S., Grabski, H., Dalle Vedove, A., Valeri, A., Sauvey, C., Ottonello, G., Summa, M., Bertozzi, S.M., Ortega, J., Bertorelli, R., Storici, P., Girotto, S., Cruciani, G., Di Martino, R.M.C., Abagyan, R., Cavalli, A.

(2026) J Med Chem 69: 9991-10018

• PubMed: 42054438 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01810
• Primary Citation Related Structures: 
  9FR5, 9FR6, 9FR7, 9FR8, 9FR9, 9FT2, 9FT3, 9FT4, 9FT6, 9FUF


• PubMed Abstract: 
  

  Accumulation of microtubule-associated protein tau is a neurotoxic hallmark in Alzheimer's disease (AD) and related tauopathies. To date, no small molecule disease-modifying therapy exists, underscoring an urgent unmet need. In this context, the multitarget-directed ligand (MTDL) approach offers a viable polypharmacological option for modulating key pathways/targets involved in tau pathology. Leveraging the interconnected roles of GSK-3β, FYN, and DYRK1A in tau hyperphosphorylation, we conducted a computational and X-ray crystallography-driven SAR exploration around our previously disclosed GSK-3β/FYN/DYRK1A inhibitor ARN25068 ( 1 ). Modification of the thieno[3,2- d ]pyrimidine central core of 1 led to the discovery of quite well-balanced GSK-3β/FYN/DYRK1A triple-targeting analogs ( 27 , 28 (ARN25699) and 31 (ARN26646)). Among these, 28 displayed a favorable ADME profile, acceptable pharmacokinetic properties, and efficacy in an in vitro tau phosphorylation assay, outperforming three single-target inhibitors tested individually or in combination. These compounds represent promising MTDL leads poised to advance therapeutic innovation in AD and related tauopathies.

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Organizational Affiliation: 
• Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy.
D3 PharmaChemistry, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, California 92093, United States.
L.A. Orbeli Institute of Physiology, National Academy of Sciences, Yerevan 0028, Armenia.
AREA Science Park, Padriciano 99, 34149 Trieste, Italy.
Protein Targets for Drug Discovery Lab, Elettra Sincrotrone Trieste S.C.p.A., SS 14 - km 163,5 in AREA Science Park, 34149 Trieste, Italy.
Molecular Horizon srl, via Montelino 20, 06084 Bettona, Italy.
Analytical Chemistry Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
Translational Pharmacology Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
Department of Chemistry, Biology and Biotechnology, University of Perugia, via dell'Elce di Sotto 8, 06123 Perugia, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.42 kDa 
• Atom Count: 2,836 
• Modeled Residue Count: 342 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A	361	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.11.23 (PDB Primary Data), 2.7.12.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627  Go to UniProtKB:  Q13627
GTEx:  ENSG00000157540

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IE6 (Subject of Investigation/LOI)	B [auth A]	3-[[[4-[(3-cyclobutyl-1~{H}-pyrazol-5-yl)amino]furo[3,2-d]pyrimidin-2-yl]amino]methyl]benzamide C21 H21 N7 O2 ZTHIMBSQDLASPC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.068	α = 90
b = 94.068	β = 90
c = 49.085	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Dalle Vedove, A., Demuro, S., Di Martino, R.M.C., Balboni, B., Tripathi, S.K., Storici, P., Girotto, S., Cavalli, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM1311991

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release
  
• Version 1.1: 2026-07-29
  Changes: Database references