SMTL ID : 6q54.1

Structure of GluA2 ligand-binding domain (S1S2J) in complex with the agonist (S)-2-Amino-3-(1-ethyl-4-hydroxy-1H-1,2,3-triazol-5-yl)propanoic acid at 1.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 Ligands: PGE.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Water bridges: A:D.65, A:S.140, A:E.145, A:R.148 Salt bridges: A:K.144, A:R.148 SO4.2: 5 residues within 4Å: Chain A: L.109, S.194, T.195, E.198, N.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.194, A:E.198, A:N.214 SO4.3: 2 residues within 4Å: Chain A: M.19, R.31 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.23, A:H.23, A:R.31 Salt bridges: A:R.31 SO4.4: 4 residues within 4Å: Chain A: K.45, H.46, K.240, Q.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.244 Water bridges: A:K.45, A:K.45 Salt bridges: A:K.45, A:H.46 SO4.5: 5 residues within 4Å: Chain A: K.20, K.21, N.22, H.23, E.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.22, A:H.23, A:E.24 Salt bridges: A:H.23 SO4.6: 2 residues within 4Å: Chain A: R.163, S.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.164 Water bridges: A:R.163 Salt bridges: A:R.163 SO4.16: 6 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 Ligands: PEG.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.140, B:S.140 Water bridges: B:S.140, B:G.141 Salt bridges: B:K.144, B:R.148 SO4.17: 1 residues within 4Å: Chain B: K.82 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.82 SO4.18: 2 residues within 4Å: Chain B: R.64, K.69 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.64, B:K.69 SO4.19: 7 residues within 4Å: Chain B: L.109, G.110, S.194, T.195, E.198, K.210, N.214 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.110, B:S.194, B:S.194, B:N.214

2 x HJ8: (2~{S})-2-azanyl-3-(3-ethyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid(Non-covalent)

HJ8.7: 16 residues within 4Å: Chain A: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.13, A:Y.61, A:L.138 Hydrogen bonds: A:P.89, A:T.91, A:S.142, A:T.143, A:E.193, A:E.193 Water bridges: A:T.143, A:T.143, A:T.143, A:Y.190 Salt bridges: A:R.96 HJ8.20: 16 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, L.192, E.193, M.196, Y.220 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:P.89, B:T.91, B:T.91, B:S.142, B:T.143, B:E.193 Water bridges: B:T.143, B:T.143, B:T.143 Salt bridges: B:R.96

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: E.27, G.28, N.29, E.30 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.27, A:N.29, A:E.30, A:E.30 Water bridges: A:N.29, A:N.29, A:N.29 GOL.21: 5 residues within 4Å: Chain A: K.151 Chain B: K.45, H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.240, B:Q.244 Water bridges: B:K.45, B:H.46 GOL.22: 5 residues within 4Å: Chain B: E.27, G.28, R.31, K.52 Ligands: PGE.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.28, B:R.31, B:R.31 Water bridges: B:Y.32 GOL.23: 3 residues within 4Å: Chain B: N.3, K.4, T.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.5, B:T.5

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 6 residues within 4Å: Chain A: K.144, R.148, W.159, R.163, F.170 Ligands: SO4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.144, A:R.148, A:W.159 PGE.24: 6 residues within 4Å: Chain B: M.19, H.23, E.24, R.31, Y.32 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.31 Water bridges: B:E.24

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 2 residues within 4Å: Chain A: I.152, A.153 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain A: I.113, S.123, A.124, G.212, G.213 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.249, N.252 Ligand excluded by PLIP

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.13: 5 residues within 4Å: Chain A: E.176, A.179, R.180, K.183, S.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.183 Water bridges: A:E.176, A:R.180 Salt bridges: A:K.183

3 x LI: LITHIUM ION(Non-covalent)

LI.14: 3 residues within 4Å: Chain A: A.2, T.5, V.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.5, H2O.3, H2O.4 LI.15: 3 residues within 4Å: Chain A: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.97, A:E.97, A:I.100, H2O.2 LI.25: 4 residues within 4Å: Chain B: E.97, I.100, D.101, F.102 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, B:I.100, H2O.16

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.26: 6 residues within 4Å: Chain B: K.144, R.148, R.149, W.159, R.163 Ligands: SO4.16 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.144, B:R.148, B:R.148, B:W.159, B:R.163, B:R.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sainas, S. et al., Use of the 4-Hydroxytriazole Moiety as a Bioisosteric Tool in the Development of Ionotropic Glutamate Receptor Ligands. J.Med.Chem. (2019)

Release Date

2019-04-17

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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