SMTL ID : 8blb.1

Human serotonin 5-HT3A receptor in complex with vortioxetine (nanodiscs, ECD, active/distorted conformation)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: I.154, N.158, I.159, S.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.142, L.187, P.188, Y.189, Y.207, V.209 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.189 NAG-NAG.3: 5 residues within 4Å: Chain B: I.154, N.158, I.159, S.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: N.142, L.187, P.188, Y.189, Y.207, V.209 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.189 NAG-NAG.5: 5 residues within 4Å: Chain C: I.154, N.158, I.159, S.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: N.142, L.187, P.188, Y.189, Y.207, V.209 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.189 NAG-NAG.7: 5 residues within 4Å: Chain D: I.154, N.158, I.159, S.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain D: N.142, L.187, P.188, Y.189, Y.207, V.209 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.189 NAG-NAG.9: 5 residues within 4Å: Chain E: I.154, N.158, I.159, S.160, F.190 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: N.142, L.187, P.188, Y.189, Y.207, V.209 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.189

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.11: 2 residues within 4Å: Chain A: D.75, N.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.76 NAG.13: 2 residues within 4Å: Chain B: D.75, N.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.76 NAG.15: 2 residues within 4Å: Chain C: D.75, N.76 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.76 NAG.17: 2 residues within 4Å: Chain D: D.75, N.76 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.76 NAG.19: 2 residues within 4Å: Chain E: D.75, N.76 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.76

5 x VTX: Vortioxetine(Non-covalent)

VTX.12: 10 residues within 4Å: Chain A: S.149, W.150, M.195, E.196, Y.201 Chain E: W.57, Y.58, R.59, Y.120, R.163 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:W.150, A:M.195, A:E.196, E:W.57, E:W.57, E:R.59, E:Y.120 Hydrogen bonds: A:W.150 pi-Stacking: E:Y.120 VTX.14: 10 residues within 4Å: Chain A: W.57, Y.58, R.59, Y.120, R.163 Chain B: S.149, W.150, M.195, E.196, Y.201 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.57, A:W.57, A:R.59, A:Y.120, B:W.150, B:M.195, B:E.196 pi-Stacking: A:Y.120 Hydrogen bonds: B:W.150 VTX.16: 10 residues within 4Å: Chain B: W.57, Y.58, R.59, Y.120, R.163 Chain C: S.149, W.150, M.195, E.196, Y.201 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.57, B:W.57, B:R.59, B:Y.120, C:W.150, C:M.195, C:E.196 pi-Stacking: B:Y.120 Hydrogen bonds: C:W.150 VTX.18: 10 residues within 4Å: Chain C: W.57, Y.58, R.59, Y.120, R.163 Chain D: S.149, W.150, M.195, E.196, Y.201 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:W.150, D:M.195, D:E.196, C:W.57, C:W.57, C:R.59, C:Y.120 Hydrogen bonds: D:W.150 pi-Stacking: C:Y.120 VTX.20: 10 residues within 4Å: Chain D: W.57, Y.58, R.59, Y.120, R.163 Chain E: S.149, W.150, M.195, E.196, Y.201 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:W.150, E:M.195, E:E.196, D:W.57, D:W.57, D:R.59, D:Y.120 Hydrogen bonds: E:W.150 pi-Stacking: D:Y.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Sanchez, U. et al., Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-15

Peptides

5-hydroxytryptamine receptor 3A: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

5-hydroxytryptamine receptor 3A