SMTL ID : 3o6h.1

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 14 PLIP interactions: 3 Ligand-Ligand interactions, 11 interactions with chain A Hydrogen bonds: E.1, E.1, E.1, A:P.89, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193 Hydrophobic interactions: A:Y.61, A:L.138 Water bridges: A:K.144, 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:K.144, B:E.193 Salt bridges: B:R.96

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

SO4.2: 2 residues within 4Å: Chain A: H.23, R.31 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.23, A:R.31 SO4.3: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:E.30 SO4.4: 4 residues within 4Å: Chain A: D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:N.72, A:G.141 Salt bridges: A:K.144, A:R.148 SO4.10: 2 residues within 4Å: Chain B: H.23, R.31 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.23, B:R.31 SO4.11: 4 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.29, B:N.29, B:E.30 SO4.12: 4 residues within 4Å: Chain B: D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:N.72, B:G.141 Salt bridges: B:K.144, B:R.148

2 x O25: 2-[({4-[(ethylamino)methyl]-3-(trifluoromethyl)-1H-pyrazol-1-yl}acetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide(Non-covalent)

O25.5: 24 residues within 4Å: Chain A: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Chain B: I.92, K.104, P.105, S.108, S.217, K.218, G.219, L.239, S.242 Ligands: DMS.6, EDO.8, O25.13, DMS.14, EDO.16 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.92, B:L.239, A:L.239 Hydrogen bonds: B:S.242 Water bridges: B:S.108, B:L.109, B:S.217 Halogen bonds: B:P.105, A:I.92 O25.13: 24 residues within 4Å: Chain A: I.92, K.104, P.105, S.108, S.217, K.218, G.219, L.239, S.242 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Ligands: O25.5, DMS.6, EDO.8, DMS.14, EDO.16 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.92, A:L.239, B:L.239 Hydrogen bonds: A:S.217, A:S.242 Water bridges: A:S.108, A:L.109, A:S.217 Halogen bonds: A:P.105, B:I.92

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 6 residues within 4Å: Chain A: S.217 Chain B: F.106, M.107, S.108 Ligands: O25.5, O25.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.108 DMS.14: 6 residues within 4Å: Chain A: F.106, M.107, S.108 Chain B: S.217 Ligands: O25.5, O25.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.108

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.214, A:S.217 Water bridges: A:S.217 EDO.8: 8 residues within 4Å: Chain A: I.92, T.93, S.217, K.218 Chain B: S.242, E.243 Ligands: O25.5, O25.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.243, A:S.217 EDO.15: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.214, B:S.217 Water bridges: B:S.217 EDO.16: 8 residues within 4Å: Chain A: S.242, E.243 Chain B: I.92, T.93, S.217, K.218 Ligands: O25.5, O25.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.243, B:S.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamieson, C. et al., A novel series of positive modulators of the AMPA receptor: structure-based lead optimization. Bioorg.Med.Chem.Lett. (2010)

Release Date

2010-09-15

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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