6KQI: Allosteric modulator

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor. Determined by X-ray diffraction at 3.25 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Homo sapiens, Pyrococcus abyssi (strain GE5 / Orsay)
Chains: 1
Atoms: 3,828
Mol. weight: 58.39 kDa
Ligands: OLC, OLA, 9GL, 9GF
Released: 23 Oct 2019

Explore 6KQI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6KQI contains 26 α-helices and 12 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 26 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	105-108	4
α-helix	113-126	14
α-helix	128-143	16
α-helix	145-148	4
α-helix	155-162	8
α-helix	165-178	14
α-helix	186-219	34
α-helix	224-227	4
α-helix	230-248	19
α-helix	263	1
β-strand	264	1	1
α-helix	265	1
β-strand	272	1	1
α-helix	273-299	27
α-helix	1009-1011	3
α-helix	1016-1027	12
β-strand	1033-1038	6	2
β-strand	1041	1	3
α-helix	1048-1058	11
α-helix	1062-1064	3
β-strand	1067-1072	6	2
β-strand	1075	1	3
α-helix	1077-1089	13
β-strand	1093-1096	4	2
α-helix	1104-1111	8
β-strand	1114-1117	4	2
β-strand	1122	1	4
α-helix	1126-1133	8
β-strand	1137-1141	5	2
β-strand	1144	1	4
α-helix	1145-1147	3
β-strand	1156-1158	3	2
α-helix	1163-1174	12
α-helix	1178-1196	19
α-helix	334-368	35
α-helix	373-382	10
α-helix	385-400	16
α-helix	402-411	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1	A	protein	492	Homo sapiens, Pyrococcus abyssi (strain GE5 / Orsay)	P21554 (AlphaFold model), Q9V2J8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6KQI_1 Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1 (chains A)
GENIQCGENFMDIECFMVLNPSQQLAIAVLSLTLGTFTVLENLLVLCVILHSRSLRCRPS
YHFIGSLAVADLLGSVIFVYSFIDFHVFHRKDSRNVFLFKLGGVTASFTAKVGSLFLAAI
DRYISIHRPLAYKRIVTRPKAVVAFCLMWTIAIVIAVLPLLGWNCEKLQSVCSDIFPHID
KTYLMFWIGVVSVLLLFIVYAYMYILWKAGIDCSFWNESYLTGSRDERKKSLLSKFGMDE
GVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHG
NVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIIT
NETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFSDQARMDIELAKTLVL
ILVVLIICWGPLLAIMVYDVFGKMNKLIKTVFAFCSMLCLLNSTVNPIIYALRSKDLRHA
FRSMFPENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	2
OLA	Oleic acid	C18 H34 O2	4
9GL	5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide	C24 H28 Cl N3 O	1
9GF	2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)ph…	C24 H40 O3	1

Water and common crystallization additives (PEG) are not listed.

Primary citation

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor. Shao, Z., Yan, W., Chapman, K. et al. Nat Chem Biol (2019) 15:1199-1205. DOI 10.1038/s41589-019-0387-2 · PubMed

Other PDB entries of the same protein (UniProt P21554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

23IV 2.42 Å, Cannabinoid Receptor 1-Gi Complex
23IW 2.42 Å, Cannabinoid Receptor 1-Gi Complex
5U09 2.6 Å, High-resolution crystal structure of the human CB1 cannabinoid receptor
7FEE 2.7 Å, Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound…
5TGZ 2.8 Å, Crystal Structure of the Human Cannabinoid Receptor CB1
5XRA 2.8 Å, Crystal structure of the human CB1 in complex with agonist AM11542
8GHV 2.8 Å, Cannabinoid Receptor 1-G Protein Complex
9B54 2.86 Å, Biased agonist bound CB1-Gi structure
8K8J 2.88 Å, Cannabinoid Receptor 1 bound to Fenofibrate coupling MiniGsq and Nb35 Complex
9ERX 2.9 Å, Structural basis of D9-THC analog activity at the Cannabinoid 1 receptor
5XR8 2.95 Å, Crystal structure of the human CB1 in complex with agonist AM841
6KPG 3.0 Å, Cryo-EM structure of CB1-G protein complex

Browse structure collections

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