SMTL ID : 5tpa.1

Structure of the human GluN1/GluN2A LBD in complex with compound 9 (GNE3500)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-oligomer

Ligands

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 10 residues within 4Å: Chain A: H.87, S.113, L.114, T.115, R.120, G.171, S.172, T.173, Y.213, D.214 14 PLIP interactions: 10 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, A:D.214, E.1, E.1, E.1, E.1 Water bridges: A:G.171 Salt bridges: A:H.87, A:R.120

1 x 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(Non-covalent)

7H2.2: 17 residues within 4Å: Chain A: I.116, V.128, P.129, F.130, V.131, E.132, T.242, G.243, L.263, V.266 Chain B: I.128, K.140, P.141, Y.144, G.250, L.270, H.273 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.141, B:Y.144, A:P.129, A:L.263, A:V.266 pi-Stacking: B:Y.144, B:Y.144, B:H.273 Halogen bonds: A:T.242

1 x GLY: GLYCINE(Non-covalent)

GLY.3: 10 residues within 4Å: Chain B: F.93, P.125, L.126, T.127, R.132, S.180, S.181, W.224, D.225, F.251 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:P.125, B:T.127, B:S.181, B:S.181, B:D.225, G.3 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Villemure, E. et al., GluN2A-Selective Pyridopyrimidinone Series of NMDAR Positive Allosteric Modulators with an Improved in Vivo Profile. ACS Med Chem Lett (2017)

Release Date

2016-11-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

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