SMTL ID : 3o28.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x O28: 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)

O28.1: 21 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, F.106, S.108, S.217, K.218, G.219, L.239, S.242 Ligands: O28.13 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.92, A:L.239 Hydrogen bonds: B:S.217 Water bridges: B:L.109, B:K.218, A:S.108 Halogen bonds: A:I.92 O28.13: 21 residues within 4Å: Chain A: I.92, K.104, P.105, F.106, 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: O28.1 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.239, A:I.92 Water bridges: B:S.108, A:L.109, A:K.218 Halogen bonds: B:I.92 Hydrogen bonds: 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 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.2, E.2, E.2 Water bridges: A:E.193 Salt bridges: A:R.96 GLU.14: 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.14, E.14, E.14 Water bridges: B:E.193 Salt bridges: B:R.96

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

SO4.3: 3 residues within 4Å: Chain A: E.24, R.31 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.31 SO4.4: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.139, A:S.140 Water bridges: A:R.148 Salt bridges: A:K.144, A:R.148 SO4.5: 4 residues within 4Å: Chain A: H.23, E.24, R.31 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.24, A:E.24 Water bridges: A:Y.32 Salt bridges: A:H.23, A:R.31 SO4.15: 3 residues within 4Å: Chain B: E.24, R.31 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.31 SO4.16: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.139, B:S.140 Water bridges: B:R.148 Salt bridges: B:K.144, B:R.148 SO4.17: 4 residues within 4Å: Chain B: H.23, E.24, R.31 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.24 Water bridges: B:Y.32 Salt bridges: B:H.23, B:R.31

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

DMS.6: 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 DMS.18: 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

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 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.8: 5 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104 Ligands: GOL.20 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.104, B:K.104, A:E.97, A:F.102 Water bridges: A:E.97 GOL.9: 2 residues within 4Å: Chain A: W.159, R.163 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain A: R.149, K.151 Chain B: E.243, Q.244 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:E.243 Hydrogen bonds: A:K.151 GOL.11: 4 residues within 4Å: Chain A: S.194, E.198, N.214, K.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:N.214, A:N.214, A:K.251 GOL.12: 4 residues within 4Å: Chain A: D.248 Chain B: N.214, D.216, S.217 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.19: 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.20: 5 residues within 4Å: Chain A: K.104 Chain B: E.97, D.101, F.102 Ligands: GOL.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.97, B:F.102, A:K.104, A:K.104 Water bridges: B:E.97 GOL.21: 2 residues within 4Å: Chain B: W.159, R.163 No protein-ligand interaction detected (PLIP) GOL.22: 4 residues within 4Å: Chain A: E.243, Q.244 Chain B: R.149, K.151 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.151 Water bridges: A:E.243 GOL.23: 4 residues within 4Å: Chain B: S.194, E.198, N.214, K.251 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.194, B:S.194, B:N.214, B:N.214, B:K.251 GOL.24: 4 residues within 4Å: Chain A: N.214, D.216, S.217 Chain B: D.248 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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