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The crystal structure of human DYRK2 in complex with curcumin

Analyse The crystal structure of human DYRK2 in complex with curcumin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZTN
Type: protein
Length: 794 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
EC: 2.7.12.1
UniProt: Q92630
Ligands: CUR
Pockets: 9 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dual specificity tyrosine-phosphorylation-regulated kinase 2 (EC 2.7.12.1)	protein	397	35% helix, 17% strand	Q92630

Ligands and binding sites

CUR · (1Z,4Z,6E)-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	872	0.76	0.80	90	CUR
2	839	0.76	0.80	82	CUR
3	222	0.56	0.79	30	empty
4	188	0.50	0.77	30	empty
5	93	0.45	0.80	21	empty

Interfaces

1 interface between chains.

A–B · 1010 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

5ZTN · The crystal structure of human DYRK2 in complex with Curcumin · the same entry in another collection · chain A against A, TM-score 1.00
Q92630 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q92630
Elsewhere: RCSB PDB 5ZTN · PDBe 5ZTN · UniProt Q92630

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