SMTL ID : 8qez.1 (1 other biounit)

Crystal structure of the AMPA receptor GluA2-L504Y-N775S ligand binding domain in complex with L-glutamate and positive allosteric modulator BPAM395 at 1.55A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 13 residues within 4Å: Chain A: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, L.192, E.193, M.196, Y.220 14 PLIP interactions: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, E.1, E.1 Water bridges: A:L.138, A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.12: 13 residues within 4Å: Chain B: Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, L.192, E.193, M.196, Y.220 13 PLIP interactions: 11 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, E.12, E.12 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.23, E.24 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.23, A:E.24 ZN.3: 4 residues within 4Å: Chain A: E.42, K.45, H.46, L.241 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.42, A:H.46, H2O.1, H2O.8, H2O.8 ZN.4: 4 residues within 4Å: Chain A: D.65, D.67 Ligands: ACT.7, ACT.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.65, A:D.65, ACT.7, ACT.9 ZN.5: 2 residues within 4Å: Chain A: D.156, W.159 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, H2O.8 ZN.13: 3 residues within 4Å: Chain B: E.42, H.46, L.241 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.42, B:H.46

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

ACT.6: 5 residues within 4Å: Chain A: A.134, R.180, S.184, K.187, Y.188 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.188 Hydrogen bonds: A:S.184, A:S.184 Water bridges: A:R.180 Salt bridges: A:R.180 ACT.7: 5 residues within 4Å: Chain A: D.65, D.67, T.68 Ligands: ZN.4, ACT.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.68 Hydrogen bonds: A:D.67 Water bridges: A:T.68 ACT.8: 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:N.214 Water bridges: A:S.217 ACT.9: 5 residues within 4Å: Chain A: D.65, A.66, D.67 Ligands: ZN.4, ACT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.67 ACT.14: 3 residues within 4Å: Chain B: E.198, E.201, K.210 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.210 Water bridges: B:K.210 ACT.15: 5 residues within 4Å: Chain B: A.134, R.180, S.184, K.187, Y.188 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.188 Hydrogen bonds: B:S.184, B:S.184 Water bridges: B:R.180 Salt bridges: B:R.180 ACT.16: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.117, B:K.117 Salt bridges: B:K.117

2 x UF5: 6-chloranyl-4-cyclopropyl-2,3-dihydrothieno[3,2-e][1,2,4]thiadiazine 1,1-dioxide(Non-covalent)

UF5.10: 15 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Chain B: I.92, P.105, S.108, S.217, K.218, G.219 Ligands: UF5.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Halogen bonds: B:S.108 Hydrogen bonds: A:P.105 UF5.18: 15 residues within 4Å: Chain A: I.92, P.105, S.108, S.217, K.218, G.219 Chain B: K.104, P.105, F.106, M.107, S.108, L.239, S.242, L.247 Ligands: UF5.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.247 Hydrogen bonds: B:P.105 Halogen bonds: A:S.108

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 6 residues within 4Å: Chain A: T.93, V.95, R.96, S.142, E.145, R.149 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: T.93, V.95, R.96, S.142, E.145 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.248, A:D.248 Water bridges: B:N.214, B:S.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francotte, P. et al., Exploring thienothiadiazine dioxides as isosteric analogues of benzo- and pyridothiadiazine dioxides in the search of new AMPA and kainate receptor positive allosteric modulators. Eur.J.Med.Chem. (2023)

Release Date

2023-12-27

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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