SMTL ID : 6sbt.1

Structure of GluK1 ligand-binding domain (S1S2) in complex with N-(7-(1H-imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl benzamide at 2.3 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: V.137, G.140, S.141, T.142, M.143, M.189, E.190 Ligands: L5H.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.141, A:T.142, A:T.142, A:E.190 Water bridges: A:V.137, A:S.141, A:L.188 SO4.2: 4 residues within 4Å: Chain A: R.31, V.53, K.54, L.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.55 Salt bridges: A:R.31, A:K.54 SO4.8: 8 residues within 4Å: Chain B: V.137, G.140, S.141, T.142, M.143, M.189, E.190 Ligands: L5H.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.141, B:T.142, B:T.142, B:E.190, B:E.190 Water bridges: B:V.137, B:S.141, B:L.188 SO4.9: 4 residues within 4Å: Chain B: R.31, V.53, K.54, L.55 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.55 Salt bridges: B:R.31, B:K.54

2 x L5H: ~{N}-[7-imidazol-1-yl-2,3-bis(oxidanylidene)-6-(trifluoromethyl)-4~{H}-quinoxalin-1-yl]benzamide(Non-covalent)

L5H.3: 16 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.88, L.89, T.90, R.95, D.139, G.140, S.141, T.144, E.190, S.193, Y.216 Ligands: SO4.1, CL.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:P.88, A:T.90, A:R.95, A:R.95 Water bridges: A:S.141 pi-Stacking: A:Y.61 L5H.10: 16 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.88, L.89, T.90, R.95, D.139, G.140, S.141, T.144, E.190, S.193, Y.216 Ligands: SO4.8, CL.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.61 Hydrogen bonds: B:P.88, B:T.90, B:R.95, B:R.95 Water bridges: B:S.141 pi-Stacking: B:Y.61

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: T.90, S.141, K.214 Ligands: L5H.3 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.75, R.81 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: T.90, S.141, K.214 Ligands: L5H.10 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: K.75, R.81 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: F.145, I.151, Y.154, I.211, D.212, S.213 Chain B: Q.238, G.241, H.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.212, A:S.213, A:S.213 Water bridges: A:S.213 GOL.7: 3 residues within 4Å: Chain A: L.12, E.13, E.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.13, A:E.14 Water bridges: A:E.13 GOL.13: 9 residues within 4Å: Chain A: Q.238, G.241, H.244 Chain B: F.145, I.151, Y.154, I.211, D.212, S.213 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.212, B:S.213, B:S.213 Water bridges: B:S.213 GOL.14: 3 residues within 4Å: Chain B: L.12, E.13, E.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.13, B:E.14 Water bridges: B:E.13, B:E.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mollerud, S. et al., N-(7-(1H-Imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)benzamide, a New Kainate Receptor Selective Antagonist and Analgesic: Synthesis, X-ray Crystallography, Structure-Affinity Relationships, and in Vitro and in Vivo Pharmacology. Acs Chem Neurosci (2019)

Release Date

2019-10-30

Peptides

Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor ionotropic, kainate 1

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