SMTL ID : 8cc6.1

Mouse serotonin 5-HT3A receptor in complex with PZ-1922

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: 4 residues within 4Å: Chain A: N.268, I.269, T.270, F.300 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.300 NAG-NAG.2: 5 residues within 4Å: Chain A: N.252, Q.299, K.301, Y.317, I.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.301, A:Y.317 NAG-NAG.3: 4 residues within 4Å: Chain B: N.268, I.269, T.270, F.300 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.300 NAG-NAG.4: 5 residues within 4Å: Chain B: N.252, Q.299, K.301, Y.317, I.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.299, B:Y.317 NAG-NAG.5: 4 residues within 4Å: Chain C: N.268, I.269, T.270, F.300 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.300 NAG-NAG.6: 3 residues within 4Å: Chain C: N.252, Y.317, I.319 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.299, C:Y.317 NAG-NAG.7: 4 residues within 4Å: Chain D: N.268, I.269, T.270, F.300 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.300 NAG-NAG.8: 5 residues within 4Å: Chain D: N.252, Q.299, K.301, Y.317, I.319 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.299, D:Y.317 NAG-NAG.9: 4 residues within 4Å: Chain E: N.268, I.269, T.270, F.300 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.300 NAG-NAG.10: 5 residues within 4Å: Chain E: N.252, Q.299, K.301, Y.317, I.319 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.299, E:K.301, E:Y.317

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

NAG.11: 2 residues within 4Å: Chain A: D.185, N.186 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: D.185, N.186 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain C: D.185, N.186 Chain D: R.138 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.138 NAG.17: 2 residues within 4Å: Chain D: D.185, N.186 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.138 NAG.20: 3 residues within 4Å: Chain A: R.138 Chain E: D.185, N.186 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:N.186, A:R.138

5 x U9L: 1-[(3-chlorophenyl)methyl]-4-piperazin-1-yl-pyrrolo[3,2-c]quinoline(Non-covalent)

U9L.12: 14 residues within 4Å: Chain A: D.146, I.148, W.167, Y.168, R.169, Y.230, R.273, D.281, S.283, I.284 Chain B: W.260, F.303, I.305, Y.311 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.148, A:W.167, A:R.169, B:F.303, B:I.305, B:Y.311 pi-Stacking: A:Y.230 Halogen bonds: A:S.283 Hydrogen bonds: B:S.259 U9L.14: 14 residues within 4Å: Chain B: D.146, I.148, W.167, Y.168, R.169, Y.230, R.273, D.281, S.283, I.284 Chain C: W.260, F.303, I.305, Y.311 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.148, B:I.148, B:W.167, B:R.169, C:F.303, C:I.305, C:Y.311 pi-Stacking: B:Y.230 Halogen bonds: B:S.283 U9L.16: 14 residues within 4Å: Chain C: D.146, I.148, W.167, Y.168, R.169, Y.230, R.273, D.281, S.283, I.284 Chain D: W.260, F.303, I.305, Y.311 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.303, D:I.305, D:Y.311, C:I.148, C:W.167, C:R.169 Hydrogen bonds: D:S.259 pi-Stacking: C:Y.230 Halogen bonds: C:S.283 U9L.18: 14 residues within 4Å: Chain D: D.146, I.148, W.167, Y.168, R.169, Y.230, R.273, D.281, S.283, I.284 Chain E: W.260, F.303, I.305, Y.311 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:I.148, D:I.148, D:W.167, D:R.169, E:F.303, E:I.305, E:Y.311 pi-Stacking: D:Y.230 Halogen bonds: D:S.283 Hydrogen bonds: E:S.259 U9L.19: 14 residues within 4Å: Chain A: W.260, F.303, I.305, Y.311 Chain E: D.146, I.148, W.167, Y.168, R.169, Y.230, R.273, D.281, S.283, I.284 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:I.148, E:W.167, E:R.169, A:F.303, A:I.305, A:Y.311 pi-Stacking: E:Y.230 Halogen bonds: E:S.283 Hydrogen bonds: A:S.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grychowska, K. et al., Superiority of the Triple-Acting 5-HT 6 R/5-HT 3 R Antagonist and MAO-B Reversible Inhibitor PZ-1922 over 5-HT 6 R Antagonist Intepirdine in Alleviation of Cognitive Deficits in Rats. J.Med.Chem. (2023)

Release Date

2023-10-11

Peptides

5-hydroxytryptamine receptor 3A: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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5-hydroxytryptamine receptor 3A

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