Crystal structure of 1-(4-(2-oxo-2-(1-PYRROLIDINYL)ETHYL)PHENYL)-3- (trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazole in complex with the ligand binding domain of the rat GLUA2 receptor and glutamate at 1.5A resolution.

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).

Ligands and binding sites

• GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
• 1NG · 1-{4-[2-oxo-2-(1-pyrrolidinyl)ethyl]phenyl}-3-( trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazole · ligand · 2 copies · chains A, C, B
• ZN · Zinc ion · metal · 5 copies · chains A, B, C
• SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 860 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 261 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

• 2XXH · Crystal structure of 1-(4-(2-oxo-2-(1-pyrrolidinyl)ethyl)phenyl)-3-(trifluoromethyl)-4,5,6… · the same entry in another collection · chain C against C, TM-score 1.00
• P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · 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 P19491
• Elsewhere: RCSB PDB 2XXH · PDBe 2XXH · UniProt P19491