SMTL ID : 3o6i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: 10 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:S.142, A:T.143, A:T.143, A:E.193, E.1, E.1, E.1 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.8: 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 13 PLIP interactions: 10 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.8, E.8, E.8 Water bridges: B:E.193 Salt bridges: B:R.96

2 x O26: 2-[({3-tert-butyl-4-[(methylamino)methyl]-1H-pyrazol-1-yl}acetyl)amino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide(Non-covalent)

O26.2: 22 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, P.105, F.106, S.217, K.218, G.219, L.239, S.242, L.247 Ligands: SO4.7, O26.9, SO4.14 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.92, A:K.218, A:L.239, B:I.92, B:L.239 Hydrogen bonds: B:S.217 Water bridges: B:S.108, B:S.217, B:S.217 O26.9: 22 residues within 4Å: Chain A: I.92, P.105, F.106, S.217, K.218, G.219, L.239, S.242, L.247 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, S.242 Ligands: O26.2, SO4.7, SO4.14 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.92, B:K.218, B:L.239, A:I.92, A:L.239 Hydrogen bonds: A:S.217 Water bridges: A:S.108, A:S.217, A:S.217

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

SO4.3: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.29, A:E.30 SO4.4: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:K.144, A:K.144, A:K.144 Salt bridges: A:K.144, A:R.148 SO4.5: 4 residues within 4Å: Chain A: H.23, E.24, R.31 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.23, A:R.31 SO4.6: 2 residues within 4Å: Chain A: R.31 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.31 SO4.7: 6 residues within 4Å: Chain A: F.106, M.107, S.108 Chain B: S.217 Ligands: O26.2, O26.9 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.108, A:S.108, B:S.217 Water bridges: A:F.106, A:L.247, A:D.248 SO4.10: 4 residues within 4Å: Chain B: E.27, G.28, N.29, E.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.29, B:E.30 SO4.11: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:K.144, B:K.144, B:K.144 Salt bridges: B:K.144, B:R.148 SO4.12: 4 residues within 4Å: Chain B: H.23, E.24, R.31 Ligands: SO4.13 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.23, B:R.31 SO4.13: 2 residues within 4Å: Chain B: R.31 Ligands: SO4.12 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.31 SO4.14: 6 residues within 4Å: Chain A: S.217 Chain B: F.106, M.107, S.108 Ligands: O26.2, O26.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.108, B:S.108, A:S.217 Water bridges: B:F.106, B:L.247, B:D.248

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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