SMTL ID : 4ymb.1

Structure of the ligand-binding domain of GluK1 in complex with the antagonist CNG10111

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x 4E7: (3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline(Non-covalent)

4E7.1: 16 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, S.173, M.189, E.190, S.193, Y.216 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.13, A:V.137 Hydrogen bonds: A:P.88, A:T.90, A:T.142, A:T.142, A:E.190, A:E.190, A:Y.216 Water bridges: A:V.137 Salt bridges: A:R.95 4E7.7: 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, S.173, M.189, E.190, S.193, Y.216 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:E.13, B:V.137 Hydrogen bonds: B:T.90, B:T.142, B:T.142, B:E.190, B:E.190, B:Y.216 Water bridges: B:V.137, B:S.141, B:T.142 Salt bridges: B:R.95

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain A: K.171, E.175 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.171, A:K.171, A:E.175 Salt bridges: A:K.171 ACT.8: 2 residues within 4Å: Chain B: K.171, E.175 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.171, B:K.171, B:K.171 Salt bridges: B:K.171 ACT.9: 6 residues within 4Å: Chain B: P.119, I.120, D.125, K.128, Q.129, I.132 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.119, B:I.120 Salt bridges: B:K.128 ACT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: Y.61, G.62, A.63, R.95 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: F.101, K.103, R.227 Chain B: F.101, K.103, R.227 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.31, F.32, K.54, L.55 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: R.31, F.32, K.54, L.55 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain A: H.80, S.224, P.225 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.83

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 2 residues within 4Å: Chain B: K.171, N.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krogsgaard-Larsen, N. et al., Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid. J.Med.Chem. (2015)

Release Date

2015-08-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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