SMTL ID : 4kfq.2 (1 other biounit)

Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x KFQ: 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one(Non-covalent)

KFQ.1: 12 residues within 4Å: Chain A: Q.13, F.92, P.124, L.125, T.126, R.131, S.179, S.180, W.223, D.224 Ligands: GOL.3, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.92, A:F.92, A:D.224 Hydrogen bonds: A:P.124, A:T.126, A:T.126, A:R.131, A:R.131, A:S.180 pi-Stacking: A:F.92

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.12, G.46, P.47, D.49, Q.61, L.86 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.12, A:P.47, A:D.49, A:Q.61 Water bridges: A:D.49, A:T.50 GOL.3: 9 residues within 4Å: Chain A: K.91, F.92, G.93, T.94, N.107, Q.178, S.179, S.180 Ligands: KFQ.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.92, A:G.93, A:N.107, A:Q.178 GOL.4: 8 residues within 4Å: Chain A: T.126, Q.144, L.146, S.180, V.181, D.224, F.250 Ligands: KFQ.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.144, A:D.224 Water bridges: A:S.180, A:S.180 GOL.5: 7 residues within 4Å: Chain A: T.33, D.37, P.38, V.39, K.40, D.69, W.284 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.37, A:K.40 Water bridges: A:T.33, A:K.40, A:K.40, A:K.40, A:D.69, A:T.283, A:T.283 GOL.6: 3 residues within 4Å: Chain A: H.12, Q.13, E.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.13, A:E.14, A:E.14 Water bridges: A:A.206 GOL.7: 1 residues within 4Å: Chain A: N.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.129 GOL.8: 2 residues within 4Å: Chain A: R.186, R.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.186, A:R.187, A:R.187 GOL.9: 4 residues within 4Å: Chain A: T.33, V.34, T.283, W.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.18, A:V.34, A:T.283 Water bridges: A:Y.18, A:F.32 GOL.10: 6 residues within 4Å: Chain A: T.157, G.158, I.159, N.160, D.161, E.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.157, A:G.158, A:N.160, A:N.160, A:D.161 Water bridges: A:I.159

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

SO4.11: 5 residues within 4Å: Chain A: N.48, S.51, S.54, R.56, V.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.48, A:N.48, A:S.51, A:S.54 Salt bridges: A:R.56 SO4.12: 4 residues within 4Å: Chain A: K.152, G.153, R.155, V.239 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.153 Water bridges: A:K.152, A:K.152 Salt bridges: A:K.152, A:R.155 SO4.13: 5 residues within 4Å: Chain A: P.167, S.168, D.169, H.197, K.200 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.197, A:K.200 SO4.14: 3 residues within 4Å: Chain A: Y.184, R.187, Q.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.188 Water bridges: A:Y.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kvist, T. et al., Crystal structure and pharmacological characterization of a novel N-methyl-D-aspartate (NMDA) receptor antagonist at the GluN1 glycine binding site. J.Biol.Chem. (2013)

Release Date

2013-10-09

Peptides

Glutamate receptor ionotropic, NMDA 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glutamate receptor ionotropic, NMDA 1

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