SMTL ID : 5zg3.3 (2 other biounits)

Crystal structure of the GluA2o LBD in complex with glutamate and TAK-137

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

1 x 9C6: 9-(4-phenoxyphenyl)-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione(Non-covalent)

9C6.1: 18 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, N.242 Chain B: K.104, P.105, M.107, S.108, S.217, K.218, G.219, L.239, N.242 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.105, A:P.105 Hydrogen bonds: A:G.219

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 11 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 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.2, E.2, E.2 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.6: 11 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 14 PLIP interactions: 3 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: E.6, E.6, E.6, B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, B:E.193 Hydrophobic interactions: B:Y.61, B:L.138 Water bridges: B:L.138 Salt bridges: B:R.96

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.23, E.24 Ligands: ACT.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.23, ACT.4 ZN.5: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ACT.10 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, ACT.10 ZN.7: 4 residues within 4Å: Chain B: E.42, H.46, L.241, Q.244 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.42, B:H.46 ZN.8: 2 residues within 4Å: Chain B: D.65 Ligands: ACT.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.65, B:D.65, ACT.9

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

ACT.4: 4 residues within 4Å: Chain A: M.19, K.20, H.23 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.23 ACT.9: 4 residues within 4Å: Chain B: D.65, D.67, T.68 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.68 ACT.10: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ZN.5 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.23 ACT.11: 5 residues within 4Å: Chain B: A.63, R.64, D.65, N.72, S.140 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.63 Hydrogen bonds: B:N.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunugi, A. et al., TAK-137, an AMPA-R potentiator with little agonistic effect, has a wide therapeutic window. Neuropsychopharmacology (2019)

Release Date

2019-01-16

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Glutamate receptor 2

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