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Crystal structure of DYRK1A in complex with 10-iodo-substituted 11H- INDOLO[3,2-C]QUINOLINE-6-carboxylic acid inhibitor 5J

Analyse Crystal structure of DYRK1A in complex with 10-iodo-substituted 11H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YLJ
Type: protein
Length: 1,390 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: 4E1, SO4
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	347	35% helix, 18% strand	Q13627
B, D	Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1)	protein	348	35% helix, 18% strand	Q13627

Ligands and binding sites

4E1 · 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid · ligand · 4 copies · chains A, B, D, C
SO4 · Sulfate ion · ion · 10 copies · chains A, B, D, C
PG4 · Tetraethylene glycol · additive · 7 copies · chains A, B, C, D

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

Pockets

16 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	1061	0.81	0.82	64	SO4
2	794	0.74	0.79	74	4E1, PG4
3	362	0.67	0.81	40	4E1
4	373	0.67	0.80	39	PG4, 4E1
5	416	0.66	0.79	42	4E1

Interfaces

3 interfaces between chains.

B–D · 661 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 569 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 319 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

4YLJ · Crystal structure of DYRK1A in complex with 10-Iodo-substituted… · 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 B 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 4YLJ · PDBe 4YLJ · UniProt Q13627

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