SMTL ID : 7wc9.1

Crystal structure of serotonin 2A receptor in complex with non-hallucinogenic psychedelic analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.207, D.211 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.207, A:D.211, A:D.211

3 x CLR: CHOLESTEROL(Non-covalent)(Non-functional Binders)

CLR.2: 10 residues within 4Å: Chain A: P.311, I.314, T.315, M.318, C.326, N.327, V.330, I.331, L.334 Ligands: OLC.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.314, A:M.318, A:V.330, A:I.331 Hydrogen bonds: A:N.327 CLR.3: 5 residues within 4Å: Chain A: A.24, I.27, M.31, Y.367, Y.372 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.27, A:I.27 Hydrogen bonds: A:Y.372 CLR.14: 2 residues within 4Å: Ligands: OLC.12, OLC.13 No protein-ligand interaction detected (PLIP)

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.4: 5 residues within 4Å: Chain A: P.78, K.80, L.81, V.84, L.149 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.80, A:V.84, A:L.149 OLC.5: 7 residues within 4Å: Chain A: M.48, I.52, L.56, Y.87, L.91, W.134, V.138 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.52, A:L.56 Hydrogen bonds: A:Y.87, A:Y.87 OLC.7: 3 residues within 4Å: Chain A: S.325, N.327 Ligands: CLR.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.327 Hydrogen bonds: A:S.325, A:N.327 OLC.8: 10 residues within 4Å: Chain A: E.7, N.9, S.11, T.15, V.18, I.69, G.72, Y.73, V.337, W.340 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.15, A:V.18, A:I.69, A:V.337, A:W.340, A:W.340 Hydrogen bonds: A:N.9 OLC.12: 13 residues within 4Å: Chain A: V.90, I.140, P.143, I.144, N.167, F.168, I.171, G.172, S.176, F.177 Ligands: 93F.6, OLC.13, CLR.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.143, A:N.167, A:F.168, A:I.171 Hydrogen bonds: A:S.176 OLC.13: 8 residues within 4Å: Chain A: I.140, P.143, F.147, K.154, D.165, F.168 Ligands: OLC.12, CLR.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.143 Hydrogen bonds: A:K.154, A:D.165

1 x 93F: (10~{R},15~{S})-12-[3-(2-methoxyphenyl)propyl]-4-methyl-1,4,12-triazatetracyclo[7.6.1.0^{5,16}.0^{10,15}]hexadeca-5(16),6,8-triene(Non-covalent)

93F.6: 14 residues within 4Å: Chain A: D.89, S.93, L.162, L.163, F.177, F.305, W.309, F.312, F.313, N.316, L.335, V.339, Y.343 Ligands: OLC.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.163, A:F.177, A:W.309, A:F.312, A:F.313, A:V.339 Salt bridges: A:D.89 pi-Stacking: A:F.177, A:F.312

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 7 residues within 4Å: Chain A: W.206, N.210, K.274, N.278, Q.282, G.285, S.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.278, A:Q.282, A:S.289, A:S.289

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

PEG.10: 7 residues within 4Å: Chain A: Y.73, S.160, L.162, D.329, G.332, A.333, N.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.160, A:N.336 PEG.11: 5 residues within 4Å: Chain A: L.39, N.41, N.44, V.297, N.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.44, A:N.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, D. et al., Structure-based discovery of nonhallucinogenic psychedelic analogs. Science (2022)

Release Date

2022-01-26

Peptides

5-hydroxytryptamine receptor 2A,5-hydroxytryptamine receptor 2A,Soluble cytochrome b562: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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5-hydroxytryptamine receptor 2A,5-hydroxytryptamine receptor 2A,Soluble cytochrome b562

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