SMTL ID : 5oew.2 (1 other biounit)

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with glutamate and positive allosteric modulator BPAM538

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 9TE: 4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

9TE.1: 18 residues within 4Å: Chain A: K.104, P.105, F.106, M.107, S.217, K.218, N.242, L.247 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, N.242 Ligands: 9TE.13 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.247, B:P.105 Hydrogen bonds: A:P.105, B:G.219 9TE.13: 18 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, N.242 Chain B: K.104, P.105, F.106, M.107, S.217, K.218, N.242, L.247 Ligands: 9TE.1 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.247, A:P.105 Hydrogen bonds: B:P.105, 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 15 PLIP interactions: 12 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:T.91, A:S.142, A:T.143, A:T.143, E.2, E.2, E.2 Water bridges: A:L.138, A:K.144, A:E.193 Salt bridges: A:R.96 GLU.14: 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: 12 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:T.91, B:S.142, B:T.143, B:T.143, E.14, E.14, E.14 Water bridges: B:L.138, B:K.144, B:E.193 Salt bridges: B:R.96

16 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 1 residues within 4Å: Chain A: H.46 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.46, H2O.5, H2O.7, H2O.8 ZN.4: 1 residues within 4Å: Chain A: D.156 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:D.156, H2O.1, H2O.7 ZN.5: 3 residues within 4Å: Chain A: H.23, E.30 Ligands: ACT.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.23, A:E.30, A:E.30, ACT.12 ZN.6: 5 residues within 4Å: Chain A: E.42, K.45, H.46, L.241, Q.244 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.42, A:H.46, H2O.1 ZN.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.8: 1 residues within 4Å: Chain A: D.126 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.126, H2O.5 ZN.9: 2 residues within 4Å: Chain A: E.132, K.187 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.132 ZN.10: 1 residues within 4Å: Chain A: E.201 No protein-ligand interaction detected (PLIP) ZN.15: 1 residues within 4Å: Chain B: H.46 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.46, H2O.12, H2O.15, H2O.15 ZN.16: 1 residues within 4Å: Chain B: D.156 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.156, B:D.156, H2O.9, H2O.15 ZN.17: 3 residues within 4Å: Chain B: H.23, E.30 Ligands: ACT.24 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.23, B:E.30, B:E.30, ACT.24 ZN.18: 5 residues within 4Å: Chain B: E.42, K.45, 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.9 ZN.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.20: 1 residues within 4Å: Chain B: D.126 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.126, H2O.13 ZN.21: 2 residues within 4Å: Chain B: E.132, K.187 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.132 ZN.22: 1 residues within 4Å: Chain B: E.201 No protein-ligand interaction detected (PLIP)

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

ACT.11: 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.12: 4 residues within 4Å: Chain A: K.20, H.23, E.30 Ligands: ZN.5 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.20, A:H.23 ACT.23: 4 residues within 4Å: Chain B: R.180, S.184, K.187, Y.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.184 Water bridges: B:R.180 Salt bridges: B:R.180 ACT.24: 4 residues within 4Å: Chain B: K.20, H.23, E.30 Ligands: ZN.17 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.20, B:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goffin, E. et al., 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides as Positive Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors with Nanomolar Potency. J. Med. Chem. (2018)

Release Date

2018-01-03

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Glutamate receptor 2

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