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Crystal structure of DYRK1A complexed with FC162 inhibitor

Analyse Crystal structure of DYRK1A complexed with FC162 inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QU2
Type: protein
Length: 1,396 residues
Chains: 4
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: JHW, SO4
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	349	38% helix, 18% strand	Q13627

Ligands and binding sites

JHW · 8-cyclopropyl-2-pyridin-3-yl-[1,3]thiazolo[5,4-f]quinazolin-9-one · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1171	0.81	0.82	81	SO4, DMS
2	390	0.66	0.79	40	JHW
3	339	0.64	0.79	38	JHW
4	361	0.64	0.79	39	JHW
5	584	0.62	0.74	44	empty

Interfaces

4 interfaces between chains.

A–D · 541 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 471 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 319 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 23 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6QU2 · Crystal structure of DYRK1A complexed with FC162 inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain C 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 6QU2 · PDBe 6QU2 · UniProt Q13627

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