SMTL ID : 7fee.1

Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 5 residues within 4Å: Chain A: G.164, F.167, K.191, A.195, I.202 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.167, A:A.195, A:I.202, A:I.202 CLR.2: 4 residues within 4Å: Chain A: L.101, V.120, L.124 Ligands: OLC.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.101, A:V.120, A:L.124

1 x 9GF: 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol(Non-covalent)

9GF.3: 17 residues within 4Å: Chain A: F.67, F.129, S.132, F.133, F.136, L.152, V.155, T.156, I.226, F.227, P.228, W.238, W.484, L.487, M.491, F.507, S.511 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.129, A:F.136, A:F.136, A:L.152, A:L.152, A:V.155, A:T.156, A:F.227, A:W.238, A:W.238, A:W.238, A:W.484, A:W.484, A:L.487, A:F.507, A:F.507 Hydrogen bonds: A:S.132, A:S.511 pi-Stacking: A:F.129, A:F.227

1 x 7IC: 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole(Non-covalent)

7IC.4: 7 residues within 4Å: Chain A: I.128, F.150, G.154, S.158, I.204, A.207, V.208 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.128, A:I.128, A:I.128, A:F.150, A:F.150, A:I.204, A:A.207, A:V.208, A:V.208 Hydrogen bonds: A:F.150, A:G.154 pi-Stacking: A:F.150

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

PEG.5: 10 residues within 4Å: Chain A: P.110, S.111, F.114, L.168, A.169, D.172, V.187, K.191, A.192, F.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.191, A:K.191 PEG.6: 7 residues within 4Å: Chain A: S.111, Y.112, I.115, L.469, T.472, R.528, S.529 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: R.109, P.110, S.111, D.172, Y.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.111, A:Y.183 GOL.8: 3 residues within 4Å: Chain A: Q.74, F.509 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74 GOL.9: 2 residues within 4Å: Chain A: Q.74 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.74 GOL.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

OLC.11: 11 residues within 4Å: Chain A: I.100, L.101, R.107, Y.112, H.113, G.116, S.117, R.189, W.200 Ligands: CLR.2, OLA.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.100, A:L.101, A:R.107, A:W.200, A:W.200 Hydrogen bonds: A:R.107 Salt bridges: A:R.107, A:R.189 OLC.12: 10 residues within 4Å: Chain A: E.92, L.95, V.96, P.522, I.523, A.526, K.530, R.533, H.534, F.536 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.95, A:V.96, A:P.522, A:I.523, A:A.526, A:R.533, A:F.536, A:F.536 Hydrogen bonds: A:K.530 Salt bridges: A:K.530, A:R.533, A:H.534

4 x OLA: OLEIC ACID(Non-covalent)

OLA.13: 1 residues within 4Å: Chain A: V.80 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.80 OLA.14: 3 residues within 4Å: Chain A: I.134, D.135, F.139 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.135, A:F.139 OLA.15: 2 residues within 4Å: Chain A: W.214, T.233 No protein-ligand interaction detected (PLIP) OLA.16: 3 residues within 4Å: Chain A: C.197, T.201 Ligands: OLC.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Molecular mechanism of allosteric modulation for the cannabinoid receptor CB1. Nat.Chem.Biol. (2022)

Release Date

2022-06-15

Peptides

Cannabinoid receptor 1,GlgA glycogen synthase: 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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Cannabinoid receptor 1,GlgA glycogen synthase