SMTL ID : 5zg1.1

Crystal structure of the GluA2o LBD in complex with glutamate and Compound-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 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: 12 interactions with chain A, 1 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.1 Water bridges: A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.7: 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 15 PLIP interactions: 4 Ligand-Ligand interactions, 11 interactions with chain B Hydrogen bonds: E.7, E.7, E.7, E.7, B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193 Hydrophobic interactions: B:Y.61, B:L.138 Water bridges: B:L.138, B:E.193 Salt bridges: B:R.96

1 x 9C0: 9-(4-~{tert}-butylphenyl)-3,4-dihydropyrido[2,1-c][1,2,4]thiadiazine 2,2-dioxide(Non-covalent)

9C0.2: 15 residues within 4Å: Chain A: K.104, P.105, S.108, S.217, K.218, L.239, N.242 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.105, B:P.105, A:P.105 Hydrogen bonds: B:G.219

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

SO4.3: 3 residues within 4Å: Chain A: L.26, E.27, R.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.27 Water bridges: A:E.24 Salt bridges: A:R.31 SO4.4: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.139, A:S.140 Water bridges: A:K.144, A:K.144, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.8: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.139, B:S.140 Water bridges: B:S.140, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.9: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:K.45 Salt bridges: B:H.46, B:K.240

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: G.62, A.63, W.71, T.93, V.95, R.96, S.142, E.145 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.62, A:T.93, A:R.96, A:E.145 Water bridges: A:R.64, A:R.148 GOL.6: 3 residues within 4Å: Chain A: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.148, A:R.163 GOL.10: 8 residues within 4Å: Chain B: G.62, A.63, W.71, T.93, V.95, R.96, S.142, E.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.62, B:T.93, B:T.93, B:R.96, B:E.145 Water bridges: B:R.64, B:R.148 GOL.11: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.216 Water bridges: A:S.217 GOL.12: 3 residues within 4Å: Chain B: R.148, W.159, R.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.148 GOL.13: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.214, B:S.217, A:D.248 Water bridges: B:S.217, B:S.217

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
A

B
B

Glutamate receptor 2

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