Structure of the ligand-binding domain of GLUK1 in complex with the antagonist CNG10111

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).

Ligands and binding sites

• 4E7 · (3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline · ligand · 2 copies · chains A, B
• CL · Chloride ion · ion · 4 copies · chains A, B
• ACT · Acetate ion · additive · 4 copies · chains A, B
• PEG · Di(hydroxyethyl)ether · additive · chains A
• EDO · 1,2-ethanediol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1056 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 4YMB · Structure of the ligand-binding domain of GluK1 in complex with the antagonist CNG10111 · the same entry in another collection · chain A against A, TM-score 1.00
• P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P22756
• Elsewhere: RCSB PDB 4YMB · PDBe 4YMB · UniProt P22756