Crystal structure of hubche with N-((1-(2,3-dihydro-1H-inden-2-yl) piperidin-3-YL)METHYL)-N-(2-(DIMETHYLAMINO)ETHYL)-2-naphthamide.

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).

Ligands and binding sites

• 92H · ~{N}-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl) piperidin-3-yl]methyl]-~{N}-[2-(dimethylamino) ethyl]naphthalene-2-carboxamide · ligand · 2 copies · chains A
• 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
• SO4 · Sulfate ion · ion · 7 copies · chains A
• CL · Chloride ion · ion · 3 copies · chains A
• GOL · Glycerol · additive · 2 copies · chains A
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
• PEG · Di(hydroxyethyl)ether · additive · chains A

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.

Modifications

Observed in the structure: 6 glycan, 3 disulfide (N-glycosylation, disulfide).

Compared structures

• 5NN0 · Crystal structure of huBChE with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-N… · the same entry in another collection · chain A against A, TM-score 1.00
• P06276 · AlphaFold monomer V2.0 prediction for cholinesterase (P06276) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P06276
• Elsewhere: RCSB PDB 5NN0 · PDBe 5NN0 · UniProt P06276