SMTL ID : 6fz4.1

Structure of GluK1 ligand-binding domain in complex with N-(7-fluoro-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)-2-hydroxybenzamide at 1.85 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.238, H.244 Chain B: I.211, D.212, S.213 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:I.211, B:S.213, A:Q.238, A:H.244 Water bridges: A:H.244 GOL.2: 5 residues within 4Å: Chain A: D.38, E.42, M.245, M.246, K.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.38 GOL.3: 5 residues within 4Å: Chain A: H.80, I.222, G.223, S.224, P.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.222 GOL.4: 2 residues within 4Å: Chain A: T.144 Ligands: EC8.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.144, A:T.144 GOL.5: 3 residues within 4Å: Chain A: N.29, L.50, Y.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.29, A:Y.51, A:Y.51 Water bridges: A:N.29 GOL.9: 5 residues within 4Å: Chain A: I.211, D.212, S.213 Chain B: Q.238, H.244 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.211, A:S.213, B:Q.238 Water bridges: B:H.244 GOL.10: 5 residues within 4Å: Chain B: D.38, E.42, M.245, M.246, K.249 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.42 GOL.11: 5 residues within 4Å: Chain B: H.80, I.222, G.223, S.224, P.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.222 GOL.12: 2 residues within 4Å: Chain B: T.144 Ligands: EC8.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.144 GOL.13: 3 residues within 4Å: Chain B: N.29, L.50, Y.51 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.29, B:Y.51, B:Y.51 Water bridges: B:N.29

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

SO4.6: 7 residues within 4Å: Chain A: V.137, G.140, S.141, T.142, M.189, E.190 Ligands: EC8.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.141, A:T.142, A:T.142, A:T.142, A:E.190 Water bridges: A:V.137, A:V.137, A:S.141, A:S.141 SO4.14: 7 residues within 4Å: Chain B: V.137, G.140, S.141, T.142, M.189, E.190 Ligands: EC8.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.141, B:T.142, B:T.142, B:T.142, B:E.190 Water bridges: B:V.137, B:V.137, B:S.141, B:E.190

2 x EC8: N-(7-fluoro-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)-2-hydroxybenzamide(Non-covalent)

EC8.7: 14 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, Y.216 Ligands: GOL.4, SO4.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.61 Hydrogen bonds: A:P.88, A:T.90, A:T.90, A:R.95, A:R.95 Water bridges: A:S.141, A:K.214 pi-Stacking: A:Y.61 pi-Cation interactions: A:K.214 EC8.15: 14 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, Y.216 Ligands: GOL.12, SO4.14 10 PLIP interactions: 10 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:T.90, B:S.141, B:K.214 pi-Stacking: B:Y.61 pi-Cation interactions: B:K.214

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

CL.8: 4 residues within 4Å: Chain A: K.103, R.227, T.231 Ligands: CL.16 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: K.103, R.227, T.231 Ligands: CL.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pallesen, J. et al., N1-Substituted Quinoxaline-2,3-diones as Kainate Receptor Antagonists: X-ray Crystallography, Structure-Affinity Relationships, and in Vitro Pharmacology. Acs Chem Neurosci (2019)

Release Date

2019-01-23

Peptides

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1

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