SMTL ID : 4kfq.1 (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.2, GOL.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.92, A:F.92, A:W.223, A:D.224 Hydrogen bonds: A:P.124, 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: 9 residues within 4Å: Chain A: T.126, Q.144, G.145, L.146, S.180, V.181, D.224 Ligands: KFQ.1, GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.126, A:T.126, A:Q.144, A:G.145, A:D.224 Water bridges: A:S.180, A:S.180 GOL.3: 7 residues within 4Å: Chain A: K.91, F.92, G.93, T.94, Q.178, S.179 Ligands: KFQ.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.92, A:G.93, A:G.93, A:Q.178 GOL.4: 6 residues within 4Å: Chain A: V.176, S.205, A.206, A.207, W.223 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.206, A:A.207 Water bridges: A:Q.13, A:Q.13 GOL.5: 2 residues within 4Å: Chain A: P.21, T.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.50 GOL.6: 4 residues within 4Å: Chain A: H.12, Q.13, E.14 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.13, A:E.14 Water bridges: A:Q.13 GOL.7: 4 residues within 4Å: Chain A: L.146, S.180, Y.184 Ligands: GOL.2 7 PLIP interactions: 7 interactions with chain A Water bridges: A:N.128, A:N.128, A:N.128, A:N.128, A:S.180, A:S.180, A:S.180 GOL.8: 7 residues within 4Å: Chain A: T.33, P.38, V.39, K.40, D.69, T.283, W.284 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.40, A:K.40, A:K.40, A:T.283 Water bridges: A:K.40, A:D.69 GOL.9: 6 residues within 4Å: Chain A: H.12, G.46, P.47, D.49, Q.61, L.86 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.12, A:G.46, A:Q.61 Water bridges: A:D.49, A:D.49 GOL.10: 4 residues within 4Å: Chain A: K.40, K.41, I.72, R.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.76

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

SO4.11: 3 residues within 4Å: Chain A: F.245, F.246, R.247 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.246, A:R.247 Salt bridges: A:R.247 SO4.12: 4 residues within 4Å: Chain A: P.55, R.56, H.57, T.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.57, A:T.58 SO4.13: 5 residues within 4Å: Chain A: P.167, S.168, D.169, H.197, K.200 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.168 Water bridges: A:D.169, A:D.169, A:H.197 Salt bridges: A:H.197, A:K.200 SO4.14: 2 residues within 4Å: Chain A: R.186, R.187 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.186, A:R.187

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
A

Glutamate receptor ionotropic, NMDA 1

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