SMTL ID : 5zg0.3 (2 other biounits)

Crystal structure of the GluA2o LBD in complex with glutamate and Compound-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

1 x 9C3: 9-{4-[(propan-2-yl)oxy]phenyl}-3,4-dihydro-2H-2lambda~6~-pyrido[2,1-c][1,2,4]thiadiazine-2,2-dione(Non-covalent)

9C3.1: 16 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, K.218, L.239, N.242 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.105, B: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 14 PLIP interactions: 11 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:K.144, A:E.193 Salt bridges: A:R.96 GLU.5: 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: 11 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, B:E.193, E.5, E.5, E.5 Water bridges: B:L.138 Salt bridges: B:R.96

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: E.42, H.46, L.241 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.42, A:H.46 ZN.4: 1 residues within 4Å: Chain A: H.23 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.23, H2O.5 ZN.6: 5 residues within 4Å: Chain B: E.42, K.45, H.46, L.241, Q.244 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.42, B:H.46 ZN.7: 2 residues within 4Å: Chain B: D.65 Ligands: ACT.10 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.65, B:D.65, H2O.9, ACT.10 ZN.8: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ACT.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, ACT.9

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

ACT.9: 3 residues within 4Å: Chain B: H.23, E.24 Ligands: ZN.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.24 Salt bridges: B:H.23 ACT.10: 4 residues within 4Å: Chain B: D.65, D.67, T.68 Ligands: ZN.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.68

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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