SMTL ID : 9mum.1

Crystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11, Glycine and Glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 10 residues within 4Å: Chain A: F.106, P.138, L.139, T.140, R.145, S.193, S.194, W.237, D.238, F.264 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:P.138, A:T.140, A:T.140, A:S.194, A:S.194, A:D.238, G.1 Salt bridges: A:R.145

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 10 residues within 4Å: Chain B: H.99, S.125, L.126, T.127, R.132, G.183, S.184, T.185, Y.225, D.226 18 PLIP interactions: 16 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.225, B:D.226 Hydrogen bonds: B:T.127, B:T.127, B:T.127, B:S.184, B:S.184, B:T.185, B:T.185, B:D.226, E.2, E.2 Water bridges: B:T.145, B:G.183, B:E.186, B:Y.256 Salt bridges: B:H.99, B:R.132

1 x 01: 5-[2-(3-chlorophenyl)-2,2-difluoroethoxy]-N-[1-(pyrazin-2-yl)cyclopropyl]pyrazine-2-carboxamide

01.3: 16 residues within 4Å: Chain A: I.141, P.154, Y.157, R.261, S.262, G.263 Chain B: F.73, P.141, F.142, V.143, E.144, L.275, V.278, M.283, E.287, L.291 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.73, B:P.141, B:E.144, B:M.283 Hydrogen bonds: B:F.142, B:E.144 pi-Stacking: A:Y.157 pi-Cation interactions: A:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bischoff, F.P. et al., Design, Synthesis, and Characterization of GluN2A Negative Allosteric Modulators Suitable for In Vivo Exploration. J.Med.Chem. (2025)

Release Date

2025-03-05

Peptides

Glutamate receptor ionotropic, NMDA 1: A
Glutamate receptor ionotropic, NMDA 2A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 1

Glutamate receptor ionotropic, NMDA 2A

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