Research workbench

Structure of DYRK1A in complex with compound 58

Analyse Structure of DYRK1A in complex with compound 58 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AKE
Type: protein
Length: 668 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
EC: 2.7.12.1
UniProt: Q13627
Ligands: RK8, CL
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	333	35% helix, 18% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	335	36% helix, 18% strand	Q13627

Ligands and binding sites

RK8 · 4-[3-[(2~{S})-2-(6-bromanylpyridin-2-yl)oxypropyl]-2-methyl-imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.84	0.85	108	RK8
2	168	0.66	0.86	24	RK8
3	90	0.45	0.79	19	empty
4	74	0.44	0.81	17	empty
5	75	0.34	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 987 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7AKE · Structure of DYRK1A in complex with compound 58 · the same entry in another collection · chain A against A, TM-score 1.00
Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q13627
Elsewhere: RCSB PDB 7AKE · PDBe 7AKE · UniProt Q13627

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.