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Structure of DYRK1A in complex with compound 51

Analyse Structure of DYRK1A in complex with compound 51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AJY
Type: protein
Length: 663 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: RKZ, CL
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 36% 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	335	36% helix, 17% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	328	36% helix, 18% strand	Q13627

Ligands and binding sites

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

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

Pockets

5 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	854	0.83	0.85	88	RKZ
2	194	0.66	0.84	25	RKZ
3	86	0.44	0.80	20	empty
4	71	0.42	0.80	17	empty
5	54	0.34	0.78	16	CL

Interfaces

1 interface between chains.

A–B · 791 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7AJY · Structure of DYRK1A in complex with compound 51 · 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 B 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 7AJY · PDBe 7AJY · UniProt Q13627

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