SMTL ID : 5zg2.1

Crystal structure of the GluA2o LBD in complex with ZK200775 and Compound-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

2 x ZK1: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid(Non-covalent)

ZK1.1: 14 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, G.141, S.142, T.174, E.193, T.195, M.196, Y.220 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:P.89, A:T.91, A:T.91, A:R.96, A:R.96, A:S.142, A:S.142, A:S.142, A:T.174 Water bridges: A:S.142, A:S.142, A:T.143, A:E.193 pi-Stacking: A:Y.61 ZK1.9: 14 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, G.141, S.142, T.174, E.193, T.195, M.196, Y.220 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.61, B:Y.61, B:Y.220 Hydrogen bonds: B:P.89, B:T.91, B:R.96, B:R.96, B:S.142, B:S.142, B:S.142 Water bridges: B:T.91, B:S.142, B:S.142, B:S.142, B:T.143, B:T.143, B:T.174 pi-Stacking: B:Y.61

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 1 residues within 4Å: Chain A: E.27 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.27, A:E.27 ZN.3: 4 residues within 4Å: Chain A: H.23 Chain B: D.139, K.144 Ligands: ACT.7 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.23, B:D.139, B:D.139, H2O.8 ZN.4: 4 residues within 4Å: Chain A: D.65, D.67 Chain B: R.31 Ligands: ACT.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.65, A:D.65, ACT.5 ZN.11: 4 residues within 4Å: Chain B: E.42, H.46, L.241, Q.244 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.42, B:H.46, H2O.13 ZN.12: 2 residues within 4Å: Chain A: S.140 Chain B: H.23 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.23, H2O.2, H2O.14, H2O.21, H2O.22

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

ACT.5: 6 residues within 4Å: Chain A: D.65, D.67, T.68 Chain B: R.31, K.52 Ligands: ZN.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:R.31, B:Y.32, B:K.52, B:K.52 Salt bridges: B:R.31 Hydrophobic interactions: A:T.68 ACT.6: 5 residues within 4Å: Chain A: R.64, K.69, W.71, V.79, Y.80 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.79, A:Y.80 Water bridges: A:R.64 Salt bridges: A:R.64 ACT.7: 6 residues within 4Å: Chain A: H.23 Chain B: D.139, K.144, R.163, F.170 Ligands: ZN.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:N.22, A:N.22, A:N.22 Salt bridges: A:H.23, B:K.144 Hydrophobic interactions: B:F.170

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.72 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:G.62, A:N.72 Water bridges: A:G.59, A:K.60, A:R.96 GOL.13: 5 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:G.62, B:N.72 Water bridges: B:G.59

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

9C0.10: 8 residues within 4Å: Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.105

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
B

B
A

Glutamate receptor 2

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