9FPX | pdb_00009fpx

Crystal structure of DYRK1A in complex with Curcumin

• PDB DOI: https://doi.org/10.2210/pdb9FPX/pdb

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


• Deposited: 2024-06-14 Released: 2025-06-25 
• Deposition Author(s): Grygier, P., Pustelny, K., Czarna, A.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 
  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Curcumin Inhibition of DYRK Kinases

Menezes, F., Grygier, P., Pustelny, K., Popowicz, G., Czarna, A.

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: 87.55 kDa 
• Atom Count: 5,258 
• Modeled Residue Count: 674 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B	371	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
PHAROS:  Q13627 GTEx:  ENSG00000157540

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CC9 (Subject of Investigation/LOI)	C [auth A], E [auth B]	curcumin C21 H20 O6 VFLDPWHFBUODDF-FCXRPNKRSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-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: 2.69 Å
• R-Value Free:  0.278 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.048	α = 90
b = 132.048	β = 90
c = 91.787	γ = 120

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: 2025-06-25 
Deposition Author(s): Grygier, P., Pustelny, K., Czarna, A.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2019/34/E/NZ1/00467

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release