8C2Z | pdb_00008c2z

Crystal structure of DYRK1B in complex with AZ191

• PDB DOI: https://doi.org/10.2210/pdb8C2Z/pdb

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


• Deposited: 2022-12-23 Released: 2024-01-17 
• Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.
• Funding Organization(s): Polish National Science Centre, National Center for Research and Development (Poland)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: in silico

Literature

Structural perspective on the design of selective DYRK1B inhibitors

Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.5 kDa 
• Atom Count: 2,884 
• Modeled Residue Count: 334 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1B	A	372	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1B, MIRK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y463 (Homo sapiens) Explore Q9Y463  Go to UniProtKB:  Q9Y463
PHAROS:  Q9Y463 GTEx:  ENSG00000105204

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QS0 (Subject of Investigation/LOI)	B [auth A]	N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine C24 H27 N7 O ZYVXTMKTGDARKR-UHFFFAOYSA-N
MN	C [auth A], D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
QS0	BindingDB:  8C2Z	Ki: 11 (nM) from 1 assay(s)
		IC50: min: 3, max: 81 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.896	α = 90
b = 121.509	β = 90
c = 54.021	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: 2024-01-17 
Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2019/34/E/NZ1/00467
National Center for Research and Development (Poland)	Poland	PPN/PPO/2018/1/00046

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary