SMTL ID : 5zg3.2 (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

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 1 residues within 4Å: Chain A: E.166 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.166, A:E.166, H2O.8 ZN.3: 4 residues within 4Å: Chain A: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:H.46, H2O.7 ZN.7: 1 residues within 4Å: Chain B: D.156 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.156 ZN.10: 4 residues within 4Å: Chain B: K.20, H.23, E.30 Ligands: ACT.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, B:E.30, B:E.30, ACT.13 ZN.11: 4 residues within 4Å: Chain B: E.42, K.45, H.46, L.241 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.16 ZN.14: 1 residues within 4Å: Chain B: E.166 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.166, B:E.166, H2O.16

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:L.138, A:E.193 Salt bridges: A:R.96 GLU.9: 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, E.9, E.9, E.9 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

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

ACT.4: 4 residues within 4Å: Chain A: R.180, S.184, K.187, Y.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.184 Water bridges: A:R.180 Salt bridges: A:R.180 ACT.5: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.248 Water bridges: B:S.217 ACT.6: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.248 ACT.12: 4 residues within 4Å: Chain B: A.134, R.180, K.187, Y.188 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.180 Salt bridges: B:R.180 ACT.13: 4 residues within 4Å: Chain B: K.20, H.23, E.30 Ligands: ZN.10 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.20, B:H.23

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)

9C6.8: 17 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, 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

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
C

B
D

Glutamate receptor 2

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