6EIJ | pdb_00006eij

DYRK1A in complex with HG-8-60-1

• PDB DOI: https://doi.org/10.2210/pdb6EIJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-19 Released: 2018-08-29 
• Deposition Author(s): Rothweiler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Novel Scaffolds for Dual Specificity Tyrosine-Phosphorylation-Regulated Kinase (DYRK1A) Inhibitors.

Czarna, A., Wang, J., Zelencova, D., Liu, Y., Deng, X., Choi, H.G., Zhang, T., Zhou, W., Chang, J.W., Kildalsen, H., Seternes, O.M., Gray, N.S., Engh, R.A., Rothweiler, U.

(2018) J Med Chem 61: 7560-7572

• PubMed: 30095246 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b01847
• Primary Citation Related Structures: 
  6EIF, 6EIJ, 6EIL, 6EIP, 6EIQ, 6EIR, 6EIS, 6EIV, 6EJ4


• PubMed Abstract: 
  

  DYRK1A is one of five members of the dual-specificity tyrosine (Y) phosphorylation-regulated kinase (DYRK) family. The DYRK1A gene is located in the Down syndrome critical region and regulates cellular processes related to proliferation and differentiation of neuronal progenitor cells during early development. This has focused research on its role in neuronal degenerative diseases, including Alzheimer's and Down syndrome. Recent studies have also shown a possible role of DYRK1A in diabetes. Here we report a variety of scaffolds not generally known for DYRK1A inhibition, demonstrating their effects in in vitro assays and also in cell cultures. These inhibitors effectively block the tau phosphorylation that is a hallmark of Alzheimer's disease. The crystal structures of these inhibitors support the design of optimized and novel therapeutics.

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Organizational Affiliation: 
• Department of Pharmacy, Faculty of Health Sciences , UiT The Arctic University of Norway , N-9037 Tromsø , Norway.
Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston , Massachusetts 02115 , United States.
The Norwegian Structural Biology Centre, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 172.48 kDa 
• Atom Count: 11,489 
• Modeled Residue Count: 1,359 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B, C, D	368	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B5Z	E [auth A], F [auth B], G [auth C], H [auth D]	~{N}-[5-[3-(2-morpholin-4-ylethylcarbamoylamino)phenyl]-[1,3]thiazolo[5,4-b]pyridin-2-yl]cyclopropanecarboxamide C23 H26 N6 O3 S NVIJYBFQLMPXOI-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 88.04	β = 90
c = 228.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Rothweiler, U.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-09-26
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary