SMTL ID : 5h8n.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 11 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, 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.1, E.1, E.1, E.1 Water bridges: A:T.115, A:T.115, A:G.171 Salt bridges: A:H.87, A:R.120

1 x 5YD: 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide(Non-covalent)

5YD.2: 15 residues within 4Å: Chain A: P.129, F.130, V.131, E.132, L.263, V.266, M.271, E.275, L.279 Chain B: I.128, P.141, Y.144, R.248, S.249, G.250 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.250, A:F.130, A:E.132 Water bridges: B:I.128 pi-Stacking: B:Y.144 pi-Cation interactions: B:R.248 Hydrophobic interactions: A:V.266, A:V.266, A:E.275, A:L.279

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain B: W.261 No protein-ligand interaction detected (PLIP)

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

Hackos, D.H. et al., Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function. Neuron (2016)

Release Date

2016-02-24

Peptides

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

Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1

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