SMTL ID : 4yma.1

Structure of the ligand-binding domain of GluA2 in complex with the antagonist CNG10109

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.144, R.148, W.159, R.163 7 PLIP interactions: 7 interactions with chain A Water bridges: A:D.139, A:K.144, A:K.144, A:K.144 Salt bridges: A:K.144, A:R.148, A:R.163 SO4.2: 3 residues within 4Å: Chain A: K.60, Y.61 Ligands: 4E5.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.61 Water bridges: A:G.62, A:G.62, A:G.62, A:G.62 Salt bridges: A:K.60 SO4.8: 2 residues within 4Å: Chain B: K.82 Ligands: SO4.10 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82 SO4.9: 2 residues within 4Å: Chain B: K.144, R.148 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.10: 2 residues within 4Å: Chain B: K.82 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82 SO4.11: 3 residues within 4Å: Chain B: K.60, Y.61 Ligands: 4E5.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.61 Water bridges: B:N.72

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: H.46, K.240 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.240, A:K.240 Water bridges: A:K.45 GOL.12: 5 residues within 4Å: Chain B: H.46, A.233, L.236, A.237, K.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.233, B:L.236, B:A.237

2 x 4E5: (3R)-3-(3-carboxy-5-hydroxyphenyl)-L-proline(Non-covalent)

4E5.4: 12 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 Ligands: SO4.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.61, A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143 Water bridges: A:R.96, A:S.140, A:S.140, A:S.142, A:T.143, A:T.143, A:T.143, A:K.144 Salt bridges: A:R.96 4E5.13: 12 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, E.193, Y.220 Ligands: SO4.11 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:P.89, B:T.91, B:T.143, B:T.143 Water bridges: B:T.91, B:S.142, B:S.142, B:K.144, B:E.193 Salt bridges: B:R.96

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

EDO.5: 2 residues within 4Å: Chain A: N.29, E.30 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.20, A:K.20, A:N.29, A:Y.32 EDO.6: 1 residues within 4Å: Chain A: K.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116 Water bridges: A:K.116

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

ACT.7: 6 residues within 4Å: Chain A: S.217 Chain B: P.105, F.106, M.107, S.108, N.242 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.242, A:S.217 Water bridges: B:S.108

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 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Glutamate receptor 2

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