Crystal structure of AP2 associated kinase 1 isoform 1 complexed with ligand (2R)-2-amino-N-[3-(difluorom ethoxy)-4-(1,3-oxazol-5-yl) phenyl]-4-methylpentanamide

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).

Ligands and binding sites

• 5QI · N-[3-(difluoromethoxy)-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide · ligand · chains A
• YFV · 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-F][1,2, 4]triazin-4-amine · ligand · chains A, B
• SO4 · Sulfate ion · ion · 6 copies · chains A, B
• PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1261 Ų buried · 24 hydrogen bonds · protein-protein

Compared structures

• 7RJ8 · Crystal structure of AP2 associated kinase 1 isoform 1 complexed with ligand… · the same entry in another collection · chain A against A, TM-score 1.00
• Q3UHJ0 · AlphaFold monomer V2.0 prediction for AP2-associated protein kinase 1 (Q3UHJ0) · a predicted model of the same protein · chain A 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 Q3UHJ0
• Elsewhere: RCSB PDB 7RJ8 · PDBe 7RJ8 · UniProt Q3UHJ0