SMTL ID : 3o29.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 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.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 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.9, E.9, E.9 Water bridges: B:E.193 Salt bridges: B:R.96

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

SO4.2: 3 residues within 4Å: Chain A: E.24, L.26, R.31 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.27, A:R.31, A:R.31 Salt bridges: A:R.31 SO4.3: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.139, A:S.140 Water bridges: A:N.72, A:S.140, A:K.144, A:K.144, A:K.144, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.10: 3 residues within 4Å: Chain B: E.24, L.26, R.31 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.27, B:R.31, B:R.31 Salt bridges: B:R.31 SO4.11: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.139, B:S.140 Water bridges: B:N.72, B:S.140, B:K.144, B:K.144, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: G.62, A.63, W.71, T.93, V.95, R.96, S.142, E.145 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.93, A:T.93, A:R.96, A:R.96, A:E.145 Water bridges: A:R.64, A:R.148 GOL.5: 5 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104 Ligands: GOL.13 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.104, A:F.102 Water bridges: B:K.104, B:N.235, B:N.235, A:T.232 GOL.6: 3 residues within 4Å: Chain A: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.163, A:R.163, A:R.163, A:R.163 GOL.7: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:N.214, B:N.214, B:S.217 Hydrogen bonds: A:D.248 GOL.12: 8 residues within 4Å: Chain B: G.62, A.63, W.71, T.93, V.95, R.96, S.142, E.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.93, B:T.93, B:R.96, B:R.96, B:E.145 Water bridges: B:R.64, B:R.148 GOL.13: 5 residues within 4Å: Chain A: K.104 Chain B: E.97, D.101, F.102 Ligands: GOL.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.104, B:F.102 Water bridges: A:K.104, A:N.235, A:N.235, B:T.232 GOL.14: 3 residues within 4Å: Chain B: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.163, B:R.163, B:R.163, B:R.163 GOL.15: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:N.214, A:N.214, A:S.217 Hydrogen bonds: B:D.248

2 x O29: N-[2-(dimethylamino)ethyl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide(Non-covalent)

O29.8: 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, L.247, D.248 Chain B: I.92, K.104, P.105, F.106, S.108, S.217, K.218, G.219, L.239 Ligands: O29.16 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.92, B:K.218, A:L.239 Water bridges: B:S.217, B:S.217, A:S.242 Salt bridges: A:D.248 Halogen bonds: A:I.92 O29.16: 22 residues within 4Å: Chain A: I.92, K.104, P.105, F.106, S.108, S.217, K.218, G.219, L.239 Chain B: I.92, P.105, F.106, M.107, S.108, S.217, K.218, G.219, L.239, S.242, L.247, D.248 Ligands: O29.8 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.92, A:K.218, B:L.239 Water bridges: A:S.217, A:S.217, B:S.242 Salt bridges: B:D.248 Halogen bonds: B:I.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jamieson, C. et al., A novel series of positive modulators of the AMPA receptor: discovery and structure based hit-to-lead studies. 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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