8T2H

DYRK1A complex with DYR530

• PDB DOI: https://doi.org/10.2210/pdb8T2H/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-06 Released: 2024-05-15 
• Deposition Author(s): Montfort, W.R., Basantes, L.E.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.213 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Discovery of DYR684, a Potent, Selective, Metabolically Stable, DYRK1A/B PROTAC utilizing a Novel Cereblon Molecular Glue

Montfort, W.R., Basantes, L.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.18 kDa 
• Atom Count: 6,053 
• Modelled Residue Count: 681 
• Deposited Residue Count: 730 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B	365	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XIR (Subject of Investigation/LOI)	C [auth A], G [auth B]	(4P)-4-{(3M)-3-[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]-2-methyl-3H-imidazo[4,5-b]pyridin-5-yl}pyridin-2-amine C23 H24 F N7 HGZWGWAZKLVNRM-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.213 
• R-Value Work: 0.163 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.472	α = 90
b = 83.213	β = 90
c = 146.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-15 
Deposition Author(s): Montfort, W.R., Basantes, L.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG067926

Revision History  

• Version 1.0: 2024-05-15
  Type: Initial release