SMTL ID : 9gib.1

NMDA bound to compound 380

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: P.129, F.130, V.131, E.132, V.266, M.271, E.275 Chain B: Y.142, R.246, S.247 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.246, A:F.130, A:E.132, A:E.132 Water bridges: B:R.246, B:G.248

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 13 residues within 4Å: Chain A: E.15, H.87, S.113, L.114, T.115, R.120, G.171, S.172, T.173, E.174, Y.213, D.214, Y.244 15 PLIP interactions: 11 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.213 Hydrogen bonds: A:T.115, A:T.115, A:S.172, A:T.173, A:D.214, E.2, E.2, E.2, E.2 Water bridges: A:S.172, A:T.173, A:E.174 Salt bridges: A:H.87, A:R.120

1 x 01: (2~{R})-2-azanyl-3-[[3-(5-ethyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid

01.3: 21 residues within 4Å: Chain A: V.266, G.267 Chain B: F.91, P.123, L.124, T.125, I.126, N.127, R.130, Q.143, G.144, L.145, S.178, S.179, V.180, Y.183, W.222, D.223, F.245, S.247, F.249 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.125, B:L.145, B:V.180, B:F.245, B:F.245, A:V.266 Hydrogen bonds: B:T.125, B:T.125, B:S.179, B:V.180, B:D.223 Water bridges: B:D.223, A:G.267 Salt bridges: B:R.130 pi-Stacking: B:F.245

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 8 residues within 4Å: Chain A: V.128, K.255, D.259, L.263 Chain B: A.131, I.134, E.135, F.136 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:F.136, B:F.136, A:D.259, A:D.259 Salt bridges: A:K.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ascic, E. et al., Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103. J.Med.Chem. (2024)

Release Date

2024-11-27

Peptides

Glutamate receptor: A
Isoform 1 of Glutamate receptor ionotropic, NMDA 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor

Isoform 1 of Glutamate receptor ionotropic, NMDA 1

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