SMTL ID : 5kdt.1

Structure of the human GluN1/GluN2A LBD in complex with GNE0723

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-oligomer

Ligands

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 4 residues within 4Å: Chain A: R.39, Y.80, E.101, R.106 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.39, A:N.53, A:N.53 Salt bridges: A:R.39

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 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: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.213, A:D.214 Hydrogen bonds: A:T.115, A:T.115, A:S.172, A:T.173, A:D.214, A:D.214, E.2, E.2 Water bridges: A:V.168, A:G.171 Salt bridges: A:H.87, A:R.120

1 x 6RV: (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile(Non-covalent)

6RV.3: 19 residues within 4Å: Chain A: I.116, P.129, F.130, V.131, E.132, T.241, T.242, G.243, V.266, M.271, E.275 Chain B: I.128, K.140, P.141, Y.144, R.248, G.250, L.270, H.273 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:P.129, A:V.266, B:P.141, B:Y.144, B:Y.144 Halogen bonds: A:T.242, B:R.248 Water bridges: B:I.128 pi-Stacking: B:Y.144, B:Y.144

1 x GLY: GLYCINE(Non-covalent)

GLY.4: 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.4 Salt bridges: B:R.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volgraf, M. et al., Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design. J. Med. Chem. (2016)

Release Date

2016-07-13

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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