SMTL ID : 6faz.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the positive allosteric modulator TDPAM01 at 1.4 A resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.139, A:S.140, A:S.140 Water bridges: A:K.144, A:K.144, A:E.145 Salt bridges: A:K.144, A:R.148 SO4.2: 1 residues within 4Å: Chain A: K.116 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.116, A:K.116 Salt bridges: A:K.116 SO4.3: 4 residues within 4Å: Chain A: E.97, D.101, F.102 Chain B: K.104 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.101, A:F.102 Water bridges: A:E.97, A:I.100, B:N.235 Salt bridges: B:K.104 SO4.15: 5 residues within 4Å: Chain B: A.63, D.139, S.140, K.144, R.148 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.139, B:S.140, B:S.140 Water bridges: B:K.144, B:E.145, B:R.148 Salt bridges: B:K.144, B:R.148 SO4.16: 1 residues within 4Å: Chain B: R.31 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.31, B:R.31, B:R.31, B:Y.32 Salt bridges: B:R.31

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

PEG.4: 4 residues within 4Å: Chain A: E.27, G.28, R.31, K.52 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.28, A:R.31, A:R.31, A:R.31, A:K.52 Water bridges: A:Y.32 PEG.5: 5 residues within 4Å: Chain A: K.20, E.33, K.253, W.254, K.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.253, A:K.258

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:R.163, A:R.163 GOL.7: 3 residues within 4Å: Chain A: H.46, K.240, Q.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.240, A:K.240, A:Q.244 Water bridges: A:K.45, A:H.46 GOL.8: 6 residues within 4Å: Chain A: S.108, S.194, T.195, E.198, K.210, N.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.210, A:N.214 Water bridges: A:E.198, A:K.251 GOL.9: 2 residues within 4Å: Chain A: K.117, M.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.117, A:K.117 GOL.17: 3 residues within 4Å: Chain B: R.148, W.159, R.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.148 Water bridges: B:W.159, B:R.163, B:R.163

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

CL.10: 2 residues within 4Å: Chain A: K.4, T.5 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: K.21, N.22, H.23, E.24 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: H.46, Q.244 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: K.50, Y.51 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: A.153 Ligand excluded by PLIP

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 3 residues within 4Å: Chain A: I.152, A.153 Chain B: K.249 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.152 Hydrogen bonds: A:A.153 Water bridges: A:V.154 Salt bridges: B:K.249 ACT.22: 5 residues within 4Å: Chain A: D.248 Chain B: N.214, L.215, D.216, S.217 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.217 ACT.23: 4 residues within 4Å: Chain A: K.104 Chain B: E.97, D.101, F.102 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.97, B:D.101, B:F.102 Salt bridges: A:K.104

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.12: 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: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.61, A:L.138 Hydrogen bonds: A:T.91, A:T.91, A:S.142, A:T.143, A:T.143, A:E.193, E.12, E.12 Water bridges: A:L.138, A:E.193, A:E.193 Salt bridges: A:R.96 GLU.24: 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: 12 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.61, B:L.138 Hydrogen bonds: B:T.91, B:T.91, B:S.142, B:T.143, B:T.143, B:E.193, E.24, E.24 Water bridges: B:L.138, B:E.193, B:E.193 Salt bridges: B:R.96

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

EDO.13: 5 residues within 4Å: Chain A: N.214, L.215, D.216, S.217 Chain B: D.248 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.214, B:D.248 Water bridges: A:S.217 EDO.25: 7 residues within 4Å: Chain B: A.134, Y.161, A.165, E.166, P.167, V.169, R.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.180 Water bridges: B:E.166, B:E.166

1 x D45: 6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)(Non-covalent)

D45.14: 18 residues within 4Å: Chain A: K.104, P.105, F.106, S.108, S.217, K.218, G.219, L.239, N.242 Chain B: K.104, P.105, F.106, S.108, S.217, K.218, G.219, L.239, N.242 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.105, A:P.105 Hydrogen bonds: B:G.219, A:G.219 Water bridges: B:N.242, B:N.242, A:L.239, A:N.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drapier, T. et al., Enhancing Action of Positive Allosteric Modulators through the Design of Dimeric Compounds. J. Med. Chem. (2018)

Release Date

2018-11-21

Peptides

Glutamate receptor 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor 2

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