Crystal structure of the neurokinin 1 receptor in complex with the small molecule antagonist netupitant

Structure

x-ray diffraction · 1 distinct chain · 67% helix, 8% strand (DSSP).

Ligands and binding sites

• OLA · Oleic acid · ligand · 9 copies · chains A
• GAW · 2-[3,5-bis(trifluoromethyl)phenyl]-~{N},2-dimethyl-~{N}-[4-(2-methylphenyl)-6-(4-methylpiperazin-1-yl) pyridin-3-yl]propanamide · ligand · chains A
• PEG · Di(hydroxyethyl)ether · additive · 24 copies · chains A
• OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 7 copies · chains A
• CIT · Citric acid · additive · chains A

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

Pockets

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

Modifications

Observed in the structure: 2 modified, 1 disulfide (alkylation, disulfide).

Compared structures

• 6HLP · Crystal structure of the Neurokinin 1 receptor in complex with the small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
• P25103 · AlphaFold monomer V2.0 prediction for substance-P receptor (P25103) · a predicted model of the same protein · chain A against A, TM-score 0.61

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 P25103
• Every structure of UniProt Q9V2J8
• Elsewhere: RCSB PDB 6HLP · PDBe 6HLP · UniProt P25103 · UniProt Q9V2J8