Structure of the human GLUN1/GLUN2A lbd in complex with compound 9 (GNE3500)

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).

Ligands and binding sites

• GLU · Glutamic acid · ligand · chains A
• 7H2 · (1R,2R)-2-(2-{[5-chloro-3-(trifluoromethyl)-1H-pyrazol-1-yl]methyl}-7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-6-yl)cyclopropane-1-carbonitrile · ligand · chains A, B
• GLY · Glycine · ligand · 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 · 1164 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 5TPA · Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500) · the same entry in another collection · chain A against A, TM-score 1.00
• Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.98
• Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B 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 Q12879
• Every structure of UniProt Q05586
• Elsewhere: RCSB PDB 5TPA · PDBe 5TPA · UniProt Q12879 · UniProt Q05586