SMTL ID : 3o2a.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x O30: N-(3-aminopropyl)-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)

O30.1: 23 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.217, K.218, G.219, L.239, S.242 Ligands: GOL.6, O30.7 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.92, B:I.92, A:L.239, A:L.247 Water bridges: B:S.217, B:S.217 Hydrogen bonds: A:M.107, A:D.248 Halogen bonds: A:G.219 O30.7: 23 residues within 4Å: Chain A: I.92, K.104, P.105, F.106, 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, L.247, D.248 Ligands: O30.1, GOL.12 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.239, B:L.247, A:I.92, A:I.92 Hydrogen bonds: B:M.107, B:D.248 Halogen bonds: B:G.219 Water bridges: A:S.217, A:S.217

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 14 PLIP interactions: 11 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, A:E.193, E.2, E.2, E.2 Water bridges: A:L.138 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 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, B:E.193, E.8, E.8, E.8 Water bridges: B:L.138 Salt bridges: B:R.96

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

SO4.3: 4 residues within 4Å: Chain A: E.24, L.26, E.27, R.31 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.27, A:R.31 Salt bridges: A:R.31 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:S.140, A:K.144, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.9: 4 residues within 4Å: Chain B: E.24, L.26, E.27, R.31 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.27, B:R.31 Salt bridges: B:R.31 SO4.10: 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:S.140, B:K.144, B:R.148 Salt bridges: B:K.144, B:R.148

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: G.62, A.63, W.71, T.93, 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.64 GOL.6: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 Ligands: O30.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:N.214, B:S.217 Hydrogen bonds: A:D.248 GOL.11: 7 residues within 4Å: Chain B: G.62, A.63, W.71, T.93, 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.64 GOL.12: 5 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 Ligands: O30.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.214, A:S.217 Hydrogen bonds: 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: 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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