SMTL ID : 8jt8.1

Crystal structure of 5-HT2AR in complex with (R)-IHCH-7179

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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

1 x EZX: 1-(4-fluorophenyl)-4-[(7R)-2,5,11-triazatetracyclo[7.6.1.0^2,7.0^12,16]hexadeca-1(15),9,12(16),13-tetraen-5-yl]butan-1-one(Non-covalent)

EZX.2: 20 residues within 4Å: Chain A: W.85, D.89, V.90, S.93, T.94, I.97, L.162, L.163, S.176, F.177, F.305, W.309, F.312, F.313, N.316, L.335, N.336, V.339, Y.343 Ligands: OLC.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.162, A:L.163, A:F.177, A:F.305, A:W.309, A:W.309, A:F.312, A:L.335 Hydrogen bonds: A:N.316, A:N.316 Salt bridges: A:D.89 pi-Stacking: A:W.309, A:W.309, A:F.312, A:F.313

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

OLC.3: 8 residues within 4Å: Chain A: T.135, V.138, G.139, M.142, P.143, V.146, F.147 Ligands: OLC.14 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.138 OLC.6: 5 residues within 4Å: Chain A: P.78, K.80, L.81, V.84, L.149 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.80, A:V.84, A:L.149 Hydrogen bonds: A:K.80 OLC.7: 6 residues within 4Å: Chain A: M.48, I.52, Y.87, L.91, W.134, V.138 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.52 Hydrogen bonds: A:Y.87 OLC.8: 3 residues within 4Å: Chain A: C.326, N.327 Ligands: CLR.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.325, A:N.327 OLC.9: 8 residues within 4Å: Chain A: N.9, S.11, T.15, I.69, Y.73, N.336, V.337, W.340 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.15, A:I.69 Hydrogen bonds: A:N.9, A:S.11 OLC.13: 12 residues within 4Å: Chain A: V.90, I.140, P.143, I.144, L.163, N.167, F.168, I.171, G.172, S.176 Ligands: EZX.2, OLC.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.143, A:N.167, A:F.168, A:I.171, A:I.171 Hydrogen bonds: A:S.176 OLC.14: 9 residues within 4Å: Chain A: I.140, P.143, F.147, K.154, D.165, F.168, V.175 Ligands: OLC.3, OLC.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.143, A:V.175 Hydrogen bonds: A:K.154, A:D.165

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.4: 10 residues within 4Å: Chain A: I.314, T.315, M.318, C.326, N.327, V.330, I.331, L.334, F.338 Ligands: OLC.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.314, A:M.318, A:V.330, A:I.331, A:L.334, A:F.338 Hydrogen bonds: A:N.327 CLR.5: 7 residues within 4Å: Chain A: I.23, A.24, I.27, L.28, M.31, Y.367, Y.372 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.23, A:A.24, A:I.27, A:I.27, A:L.28 Hydrogen bonds: A:Y.372

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

1PE.10: 5 residues within 4Å: Chain A: W.206, K.274, N.278, Q.282, G.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.274, A:K.274, A:N.278, A:Q.282

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

PEG.11: 5 residues within 4Å: Chain A: Y.73, S.160, D.329, G.332, N.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.160, A:S.160, A:N.336 PEG.12: 6 residues within 4Å: Chain A: L.39, N.44, A.294, V.297, N.357, Y.360 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

Chen, Z. et al., Flexible scaffold-based cheminformatics approach for polypharmacological drug design. Cell (2024)

Release Date

2024-02-28

Peptides

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,Soluble cytochrome b562

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