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DYRK1A in complex with XMD8-49

Analyse DYRK1A in complex with XMD8-49 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6EIL
Type: protein
Length: 1,348 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DYRK1A
UniProt: Q13627
Ligands: B6B
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DYRK1A	protein	342	36% helix, 18% strand	Q13627
B	DYRK1A	protein	340	34% helix, 18% strand	Q13627
C	DYRK1A	protein	333	38% helix, 16% strand	Q13627
D	DYRK1A	protein	333	38% helix, 19% strand	Q13627

Ligands and binding sites

B6B · [3-azanyl-6-(5-azanyl-2-methoxy-phenyl)pyrazin-2-yl]-pyridin-3-yl-methanone · ligand · 3 copies · chains A, B, D

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.87	0.88	131	empty
2	1163	0.84	0.84	116	empty
3	834	0.77	0.80	79	B6B
4	908	0.76	0.79	92	empty
5	561	0.73	0.81	58	empty

Interfaces

6 interfaces between chains.

A–B · 1221 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1191 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 964 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 854 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

6EIL · DYRK1A in complex with XMD8-49 · 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 6EIL · PDBe 6EIL · UniProt Q13627

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