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Human DYRK1A in complex with ldn-211898

Analyse Human DYRK1A in complex with ldn-211898 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5AIK
Type: protein
Length: 1,374 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DYRK1A dual-specificity tyrosine-phosphorylation regulated kinase 1A
EC: 2.7.11.1
UniProt: Q13627
Ligands: AWR, PO4
Pockets: 15 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DYRK1A dual-specificity tyrosine-phosphorylation regulated kinase 1A (EC 2.7.11.1)	protein	345	36% helix, 18% strand	Q13627
B, C	DYRK1A dual-specificity tyrosine-phosphorylation regulated kinase 1A (EC 2.7.11.1)	protein	343	35% helix, 18% strand	Q13627
D	DYRK1A dual-specificity tyrosine-phosphorylation regulated kinase 1A (EC 2.7.11.1)	protein	343	36% helix, 18% strand	Q13627

Ligands and binding sites

AWR · 4-(7-METHOXY-1-(TRIFLUOROMETHYL)-9H-PYRIDO[3,4-B]INDOL-9-yl)butan-1-amine · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 10 copies · chains A, D, B, C

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

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1064	0.84	0.85	93	empty
2	931	0.78	0.80	84	AWR, PO4
3	1075	0.77	0.79	91	AWR, PO4
4	339	0.65	0.80	32	AWR
5	282	0.62	0.80	31	AWR

Interfaces

4 interfaces between chains.

A–D · 1044 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 758 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 591 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 43 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

5AIK · Human DYRK1A in complex with LDN-211898 · 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 5AIK · PDBe 5AIK · UniProt Q13627

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