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DYRK1A with PST001

Analyse DYRK1A with PST001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YF8
Type: protein
Length: 1,346 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: OPW
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · 4 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	342	35% helix, 18% strand	Q13627
B	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	340	35% helix, 17% strand	Q13627
C	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	333	36% helix, 17% strand	Q13627
D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	331	36% helix, 19% strand	Q13627

Ligands and binding sites

OPW · ~{N}-[5-(5-methoxy-1,3-benzothiazol-2-yl)pyridin-3-yl]ethanamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	930	0.85	0.86	93	empty
2	989	0.84	0.85	86	empty
3	1093	0.77	0.79	96	OPW
4	975	0.76	0.79	94	OPW
5	637	0.74	0.81	58	empty

Interfaces

5 interfaces between chains.

A–B · 1279 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1255 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 882 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 828 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 35 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).

Compared structures

6YF8 · DYRK1A with PST001 · 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 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 6YF8 · PDBe 6YF8 · UniProt Q13627

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