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Structure of DYRK1A in complex with compound 1

Analyse Structure of DYRK1A in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A4R
Type: protein
Length: 670 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: QY8
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	337	36% helix, 18% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	333	36% helix, 18% strand	Q13627

Ligands and binding sites

QY8 · 2-amino-3H,4H,7H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 2 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	942	0.83	0.85	105	QY8, DMS
2	76	0.44	0.81	18	DMS
3	76	0.41	0.79	19	empty
4	73	0.40	0.79	18	empty
5	54	0.31	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 912 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

7A4R · Structure of DYRK1A in complex with compound 1 · 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 0.98

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 7A4R · PDBe 7A4R · UniProt Q13627

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