SMTL ID : 8jt6.1

5-HT1A-Gi in complex with compound (R)-IHCH-7179

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 16 residues within 4Å: Chain E: Y.157, T.161, L.164, L.165, L.168, Q.219, L.502, A.505, I.506, W.509, L.510, S.513, L.516, L.517 Ligands: CLR.2, CLR.6 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.164, E:L.502, E:A.505, E:I.506, E:W.509, E:L.516 Hydrogen bonds: E:Q.219 CLR.2: 12 residues within 4Å: Chain E: V.466, K.467, G.470, I.471, G.474, T.475, L.478, C.479, L.510, S.513, L.517 Ligands: CLR.1 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.467, E:I.471, E:L.478, E:L.517 CLR.3: 9 residues within 4Å: Chain E: V.180, A.184, V.202, L.205, M.206, V.209, L.210 Ligands: CLR.4, PLM.7 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.205, E:V.209 CLR.4: 10 residues within 4Å: Chain E: Y.195, S.199, V.202, M.206, P.272, A.276, I.279, W.283 Ligands: CLR.3, PLM.5 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.276, E:I.279 CLR.6: 10 residues within 4Å: Chain E: L.164, T.167, L.168, C.171, L.516, L.517, V.520, F.525 Ligands: CLR.1, J40.8 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.167, E:L.168, E:F.525

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 8 residues within 4Å: Chain E: R.273, A.276, A.277, I.279, S.280, W.283, F.287 Ligands: CLR.4 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.283, E:F.287 PLM.7: 9 residues within 4Å: Chain E: V.173, A.177, V.180, A.181, A.184, L.185, L.205, V.209 Ligands: CLR.3 No protein-ligand interaction detected (PLIP)

1 x J40: [(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate(Non-covalent)

J40.8: 14 residues within 4Å: Chain A: C.351, G.352 Chain E: R.256, K.464, K.467, T.468, I.471, I.472, I.521, Y.524, F.525, N.526, K.527 Ligands: CLR.6 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:T.468, E:F.525, E:F.525, E:K.527, A:C.351 Salt bridges: E:R.256, E:K.464, E:K.467, E:K.467, E:K.527

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.9: 20 residues within 4Å: Chain E: A.215, Y.218, Q.219, F.234, I.235, D.238, V.239, C.242, T.243, I.246, I.289, C.309, I.311, S.321, A.325, W.480, F.483, F.484, N.508, Y.512 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:A.215, E:Y.218, E:Y.218, E:F.234, E:F.234, E:I.311 Hydrogen bonds: E:T.243, E:T.243 Salt bridges: E:D.238 pi-Stacking: E:F.484 Halogen bonds: E:Q.219

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

Guanine nucleotide-binding protein G(i) subunit alpha-1: A
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1: B
ScFv16: C
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2: D
Soluble cytochrome b562,5-hydroxytryptamine receptor 1A: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
G

E
R

Membrane

We predict this structure to be a membrane protein.
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Guanine nucleotide-binding protein G(i) subunit alpha-1

Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

ScFv16

Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

Soluble cytochrome b562,5-hydroxytryptamine receptor 1A

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