SMTL ID : 3o6g.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.10: 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.10, E.10, E.10 Water bridges: 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.46, K.240 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.46, A:K.240 SO4.3: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.140 Water bridges: A:K.144, A:K.144, A:R.148, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.4: 1 residues within 4Å: Chain A: R.149 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.149, A:R.149, A:R.149 Salt bridges: A:R.149 SO4.11: 2 residues within 4Å: Chain B: H.46, K.240 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.46, B:K.240 SO4.12: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.140 Water bridges: B:K.144, B:K.144, B:R.148, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.13: 1 residues within 4Å: Chain B: R.149 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.149, B:R.149, B:R.149 Salt bridges: B:R.149

2 x O27: N-[(3R)-pyrrolidin-3-yl]-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)

O27.5: 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.217, K.218, G.219, L.239, S.242 Ligands: O27.14 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.105, A:L.239, B:I.92, B:K.218 Hydrogen bonds: A:F.106, A:M.107 Water bridges: A:L.247, B:L.109 Halogen bonds: A:G.219 O27.14: 22 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: O27.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.105, B:L.239, A:I.92, A:K.218 Hydrogen bonds: B:F.106, B:M.107 Water bridges: B:L.247, A:L.109 Halogen bonds: B:G.219

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

EDO.6: 3 residues within 4Å: Chain A: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.159, A:R.163 EDO.7: 2 residues within 4Å: Chain A: R.149 Chain B: E.243 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.243, B:E.243, B:E.243 EDO.8: 5 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, C.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.117 EDO.9: 4 residues within 4Å: Chain A: P.120, I.121, E.122, D.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.126 EDO.15: 3 residues within 4Å: Chain B: R.148, W.159, R.163 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.159, B:R.163 EDO.16: 2 residues within 4Å: Chain A: E.243 Chain B: R.149 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.243, A:E.243, A:E.243 EDO.17: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.117 EDO.18: 4 residues within 4Å: Chain B: P.120, I.121, E.122, D.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.126

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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