SMTL ID : 6q60.1

Structure of GluA2 ligand-binding domain (S1S2J) in complex with the agonist (S)-2-Amino-3-(2-methyl-5-hydroxy-2H-1,2,3-triazol-4-yl)propanoic acid at 1.55 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

HJH.1: 14 residues within 4Å: Chain A: 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:E.193 Water bridges: A:T.143, A:T.143, A:T.143 Salt bridges: A:R.96 HJH.13: 14 residues within 4Å: Chain B: 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:T.143, B:E.193 Water bridges: B:S.142, B:T.143, B:T.143 Salt bridges: B:R.96

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

SO4.2: 6 residues within 4Å: Chain A: A.63, D.139, S.140, G.141, K.144, R.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.139, A:S.140, A:S.140, A:S.140 Water bridges: A:G.141 Salt bridges: A:K.144, A:R.148 SO4.3: 2 residues within 4Å: Chain A: M.19, R.31 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.23, A:H.23, A:R.31, A:Y.32 Salt bridges: A:R.31 SO4.14: 2 residues within 4Å: Chain B: K.116, K.185 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.116, B:K.116 Salt bridges: B:K.116 SO4.15: 6 residues within 4Å: Chain B: A.63, D.139, S.140, G.141, K.144, R.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.140, B:S.140, B:S.140 Water bridges: B:G.141 Salt bridges: B:K.144, B:R.148

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.217, A:D.248 Water bridges: B:S.217, A:D.248, A:D.248 GOL.5: 9 residues within 4Å: Chain A: S.108, L.109, G.110, S.194, T.195, E.198, K.210, N.214, K.251 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.194, A:E.198, A:K.210, A:N.214 GOL.6: 8 residues within 4Å: Chain A: I.113, E.122, S.123, A.124, E.125, G.212, G.213, L.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.124, A:G.213, A:G.213 GOL.7: 3 residues within 4Å: Chain A: R.148, W.159, R.163 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:W.159, A:R.163, A:R.163 GOL.8: 8 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104, N.232, N.235 Ligands: LI.12, GOL.18 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.97, A:D.101, A:D.101, A:F.102, B:K.104 Water bridges: B:N.232, B:N.232, B:N.235, B:N.235 GOL.9: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.214, A:D.216, A:S.217, A:S.217 Water bridges: A:N.214, A:N.214, A:S.217, B:D.248, B:D.248 GOL.16: 4 residues within 4Å: Chain B: M.19, H.23, E.24, R.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.23, B:R.31 Water bridges: B:E.24 GOL.17: 3 residues within 4Å: Chain B: G.28, R.31, K.52 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.31, B:R.31, B:K.52 Water bridges: B:E.27 GOL.18: 7 residues within 4Å: Chain A: K.104, N.235 Chain B: E.97, D.101, F.102 Ligands: GOL.8, LI.23 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.97, B:F.102, A:K.104 Water bridges: B:D.101, B:D.101, B:D.101, B:D.101, A:N.232, A:N.235, A:N.235 GOL.19: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.46, B:K.240, B:Q.244 Water bridges: B:H.46, B:Q.244 GOL.20: 3 residues within 4Å: Chain B: R.148, W.159, R.163 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.148, B:R.148, B:W.159, B:R.163, B:R.163 GOL.21: 6 residues within 4Å: Chain A: L.94, E.98 Chain B: H.46, L.236, A.237, K.240 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.98, B:H.46, B:L.236, B:K.240 Water bridges: B:H.46

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

CL.10: 3 residues within 4Å: Chain A: K.21, N.22, H.23 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: I.152, A.153 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: K.4, T.5 Ligand excluded by PLIP

2 x LI: LITHIUM ION(Non-covalent)

LI.12: 5 residues within 4Å: Chain A: E.97, I.100, D.101, K.226 Ligands: GOL.8 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.23: 4 residues within 4Å: Chain B: E.97, I.100, D.101 Ligands: GOL.18 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, B:I.100, H2O.17

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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