SMTL ID : 3s2v.1

Crystal Structure of the Ligand Binding Domain of GluK1 in Complex with an Antagonist (S)-1-(2'-Amino-2'-carboxyethyl)-3-[(2-carboxythien-3-yl)methyl]thieno[3,4-d]pyrimidin-2,4-dione at 2.5 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x 3HU: (S)-1-(2'-AMINO-2'-CARBOXYETHYL)-3-[(2-CARBOXYTHIEN-3-YL)METHYL]THIENO[3,4-D]PYRIMIDIN-2,4-DIONE(Non-covalent)

3HU.1: 14 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.88, L.89, T.90, R.95, V.137, S.141, T.142, M.189, E.190, S.193, Y.216 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:P.88, A:T.90, A:T.90, A:T.90, A:S.141, A:T.142, A:E.190, A:S.193 Water bridges: A:G.62, A:V.137, A:M.143, A:E.190 Salt bridges: A:R.95 3HU.4: 16 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, M.189, E.190, S.193, Y.216 Ligands: CL.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:P.88, B:T.90, B:T.90, B:S.141, B:S.141, B:T.142, B:E.190, B:S.193 Water bridges: B:T.90, B:T.142, B:M.143 Salt bridges: B:R.95

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

SO4.2: 4 residues within 4Å: Chain A: D.212, S.213 Chain B: Q.238, H.244 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.238, A:D.212, A:S.213 Water bridges: B:H.244 Salt bridges: B:H.244 SO4.5: 5 residues within 4Å: Chain A: Q.238, H.244 Chain B: Y.154, D.212, S.213 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.238, B:Y.154, B:D.212, B:S.213 Salt bridges: A:H.244 SO4.6: 3 residues within 4Å: Chain B: R.115, L.181, N.203 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.203 Salt bridges: B:R.115

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: K.171 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.171, A:E.175 GOL.8: 3 residues within 4Å: Chain B: P.25, L.26, Y.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.26, B:L.26

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

CL.7: 3 residues within 4Å: Chain B: N.172, S.173 Ligands: 3HU.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Venskutonyte, R. et al., Selective kainate receptor (GluK1) ligands structurally based upon 1H-cyclopentapyrimidin-2,4(1H,3H)-dione: synthesis, molecular modeling, and pharmacological and biostructural characterization. J.Med.Chem. (2011)

Release Date

2011-06-22

Peptides

Glutamate receptor, ionotropic kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor, ionotropic kainate 1

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