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6kqi

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor

Method: X-RAY DIFFRACTION Dmax: 104.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1

Homo sapiens

UniProt P21554

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 94–301 Chain A； UniProt 333–413 Fragment：C1 Mutation：S203K,T210A,E273K,T283V,R340E 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 9GL 5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide × 1 OLA OLEIC ACID × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6；293 K；33% PEG 400, 100mM Sodium Cacodylate pH 6.0, 100mM Sodium Malonate Resolution 3.25 Å R-free 0.312

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6KQI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LVQ IC3 of CB1 Bound to G(alpha)i Deposited 2002-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 338–346（9 aa） Fragment：IC3 of CB1 (residues 338-346)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 10 mM acetate；Pressure 1
NMR sample composition LAKT peptide at 4.0 mM, G(alpha)i at 200 uM. | 10 mM acetate buffer, pH 6.0, 1 mM DTT, TSP
Resolution not provided
1LVR IC3 of CB1 (L431A,A432L) Bound to G(alpha)i Deposited 2002-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 338–346（9 aa） Fragment：IC3 of CB1(residues 338-346)
Mutation：L4A,A5L No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；308 K；Ionic strength (raw mmCIF value) 10 mM acetate buffer；Pressure 1
NMR sample composition ALKT 4.0 mM G(alpha)i 200 uM | acetate buffer, 10 mM
Resolution not provided
23IV Cannabinoid Receptor 1-Gi Complex Deposited 2026-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–472（472 aa）
Not recorded A1E5S methyl 1-[[1-[(4-fluorophenyl)methyl]indazol-3-yl]carbonylamino]cyclopropane-1-carboxylate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
23IW Cannabinoid Receptor 1-Gi Complex Deposited 2026-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded A1E5T methyl (2~{S},3~{R})-2-[[1-[(4-fluorophenyl)methyl]indazol-3-yl]carbonylamino]-3-oxidanyl-butanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
2B0Y Solution Structure of a peptide mimetic of the fourth cytoplasmic loop of the G-protein coupled CB1 cannabinoid receptor Deposited 2005-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 400–416（17 aa） Fragment：Fragment of the C-terminal juxtramembrane region of CB1 Cannabinoid receptor(Intracellular 4th loop region CB1 401-417)
Mutation：C16S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；310 K；Ionic strength (raw mmCIF value) no salts used；Pressure ambient
NMR sample composition 5 mM sample in H2O (9:1 H2O/2H2O, pH 3.0). | 70 mM SDS
Resolution not provided
2KOE Human cannabinoid receptor 1 - helix 7/8 peptide Deposited 2009-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 377–416（40 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 310 K；Pressure ambient
NMR sample composition 1 mM peptide, 30 % TFE, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
5TGZ Crystal Structure of the Human Cannabinoid Receptor CB1 Deposited 2016-09-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 99–306（208 aa） Fragment：UNP RESIDUES 99-306,UNP RESIDUES 2-148,UNP RESIDUES 332-414
Chain A 332–414（83 aa） Fragment：UNP RESIDUES 99-306,UNP RESIDUES 2-148,UNP RESIDUES 332-414
Mutation：T210A, E273K, T283V,P1002A, Y1098W,R340E Mutation：T210A, E273K, T283V,P1002A, Y1098W,R340E ZDG 4-[4-[2-(2,4-dichlorophenyl)-4-methyl-5-(piperidin-1-ylcarbamoyl)pyrazol-3-yl]phenyl]but-3-ynyl nitrate × 1 FMN FLAVIN MONONUCLEOTIDE × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 OLA OLEIC ACID × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.1M HEPES pH 7.0-7.4, 100mM (NH4)2HPO4, 25%-32% PEG 400, 2-20 mM Ethylenediaminetetraacetic acid disodium salt dehydrate (EDTA)
Resolution 2.80 Å R-free 0.238
5U09 High-resolution crystal structure of the human CB1 cannabinoid receptor Deposited 2016-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 90–301（212 aa） Fragment：P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413
Chain A 333–421（89 aa） Fragment：P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413
Mutation：T210A Mutation：T210A PEG DI(HYDROXYETHYL)ETHER × 9 SO4 SULFATE ION × 4 7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate
Resolution 2.60 Å R-free 0.238
5XR8 Crystal structure of the human CB1 in complex with agonist AM841 Deposited 2017-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 99–306（208 aa） Fragment：;UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414 ;
Chain A 332–414（83 aa） Fragment：;UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414,UNP residues 99-306,UNP residues 3-148,UNP residues 332-414 ;
Mutation：T210A,E273K,T283V,Y1098W,R340E Mutation：T210A,E273K,T283V,Y1098W,R340E FMN FLAVIN MONONUCLEOTIDE × 1 8D0 (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol × 1 CLR CHOLESTEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.2；293 K；0.1 M sodium cacodylate trihydrate pH 6.2, 120 mM C6H5Na3O7, 30% PEG400 and 100 mM Glycine
Resolution 2.95 Å R-free 0.274
5XRA Crystal structure of the human CB1 in complex with agonist AM11542 Deposited 2017-06-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 99–306（208 aa） Fragment：UNP residues 99-306,UNP residues 3-148,UNP residues 332-414
Chain A 332–414（83 aa） Fragment：UNP residues 99-306,UNP residues 3-148,UNP residues 332-414
Mutation：T210A, E273K, T283V,Y1098W,R340E Mutation：T210A, E273K, T283V,Y1098W,R340E FMN FLAVIN MONONUCLEOTIDE × 1 8D3 (6aR,10aR)-3-(8-bromanyl-2-methyl-octan-2-yl)-6,6,9-trimethyl-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol × 1 OLA OLEIC ACID × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 1 CLR CHOLESTEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；0.1 M sodium cacodylate trihydrate pH 6.4, 300-350 mM C4H4KNaO6, 30% PEG400
Resolution 2.80 Å R-free 0.252
6KPG Cryo-EM structure of CB1-G protein complex Deposited 2019-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 71–425（355 aa）
Mutation：E273K, T283V, R340E 8D0 (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6N4B Cannabinoid Receptor 1-G Protein Complex Deposited 2018-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded KCA methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate × 1 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7FEE Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1 Deposited 2021-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 74–89（16 aa）
Chain A 90–305（216 aa）
Chain A 333–414（82 aa）
Mutation：S203K,T210A,E273K,T283V,R340E,N393D Mutation：S203K,T210A,E273K,T283V,R340E,N393D Mutation：S203K,T210A,E273K,T283V,R340E,N393D CLR CHOLESTEROL × 2 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 7IC 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 OLA OLEIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；25-36% PEG 300, 100Mm MES pH 6.0, 120-190mM Magnesium Sulfate
Resolution 2.70 Å R-free 0.319
7V3Z Structure of cannabinoid receptor type 1(CB1) Deposited 2021-08-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 102–306（205 aa）
Chain A 336–414（79 aa）
Mutation：H154L,T210A,E273K,T283V,Y1098W,R340E Mutation：H154L,T210A,E273K,T283V,Y1098W,R340E 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 CLR CHOLESTEROL × 1 FMN FLAVIN MONONUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.2；293.15 K；30% PEG400, 100 mM HEPES sodium pH 7.2, 80-100mM sodium citrate tribasic dihydrate
Resolution 3.29 Å R-free 0.276
7WV9 Allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1 in complex with Gi protein Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 7IC 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8GAG Cannabinoid receptor 1-Gi complex with novel ligand Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded YVF methyl (2R)-2-({(1M)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1H-pyrazole-3-carbonyl}amino)-2-(thiophen-2-yl)propanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8GHV Cannabinoid Receptor 1-G Protein Complex Deposited 2023-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–472（472 aa）
Not recorded ZI5 (5Z,8Z,11Z,13S,14Z)-N-[(2R)-1-hydroxypropan-2-yl]-13-methylicosa-5,8,11,14-tetraenamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8IKG Cryo-EM structure of human receptor with G proteins Deposited 2023-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 99–408（310 aa）
Not recorded Q2B 3-[(1S)-1-(furan-2-yl)-2-nitro-ethyl]-2-phenyl-1H-indole × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8IKH Cryo-EM structure of human receptor with G proteins Deposited 2023-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 99–408（310 aa）
Not recorded Q2L 3-[(1R)-1-(2-methoxyphenyl)-2-nitro-ethyl]-2-phenyl-1H-indole × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8K8J Cannabinoid Receptor 1 bound to Fenofibrate coupling MiniGsq and Nb35 Complex Deposited 2023-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 71–425（355 aa）
Not recorded J3O Fenofibrate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.88 Å
8WRZ Cry-EM structure of cannabinoid receptor-beta-arrestin-1 complex Deposited 2023-10-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 71–432（362 aa）
Mutation：M29W, H124I, T210I, E273K, T283V, R340E 8D0 (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8WU1 Cryo-EM structure of CB1-beta-arrestin1 complex Deposited 2023-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–413（413 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) KCA methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B54 Biased agonist bound CB1-Gi structure Deposited 2024-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded A1AIW methyl N-{6-(4-carbamimidamidobutoxy)-1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9B65 Biased agonist bound CB1-Gi structure Deposited 2024-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded KCA methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9B9Y Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 96–301（206 aa）
Chain R 333–416（84 aa）
Not recorded 7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9B9Z Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 96–301（206 aa）
Chain R 333–416（84 aa）
Not recorded A1AKO (4S)-3-(4-chlorophenyl)-N'-[(1E)-ethanimidoyl]-4-phenyl-N-[4-(trifluoromethyl)benzene-1-sulfonyl]-4,5-dihydro-1H-pyrazole-1-carboximidamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BA0 Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 96–301（206 aa）
Chain R 333–416（84 aa）
Not recorded A1AKN N-(N-{(E)-[(4S)-3-(4-chlorophenyl)-4-phenyl-4,5-dihydro-1H-pyrazol-1-yl][4-(trifluoromethyl)benzene-1-sulfonamido]methylidene}carbamimidoyl)acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9DGI Cannabinoid receptor 1-Gi complex with novel ligand Deposited 2024-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain R 1–472（472 aa）
Not recorded YVF methyl (2R)-2-({(1M)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1H-pyrazole-3-carbonyl}amino)-2-(thiophen-2-yl)propanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
9EGO Cannabinoid receptor 1-Gi complex with novel ligand Deposited 2024-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–472（472 aa）
Not recorded YVF methyl (2R)-2-({(1M)-5-methyl-1-[3-(trifluoromethyl)phenyl]-1H-pyrazole-3-carbonyl}amino)-2-(thiophen-2-yl)propanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9ERX Structural basis of D9-THC analog activity at the Cannabinoid 1 receptor Deposited 2024-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–472（471 aa）
Not recorded A1H66 (6aR,10aR)-9-(hydroxymethyl)-6,6-dimethyl-3-(2-methyloctan-2-yl)-6a,7,10,10a-tetrahydrobenzo[c]chromen-1-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

30 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CNR1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–209； UniProt 94–301 Author chain A； PDBConstruct 406–486； UniProt 333–413

Cannabinoid receptor 1,GlgA glycogen synthase,Cannabinoid receptor 1

Homo sapiens

UniProt Q9V2J8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 218–413 Fragment：C1 Mutation：S203K,T210A,E273K,T283V,R340E 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 9GL 5-chloro-3-ethyl-N-{2-[4-(piperidin-1-yl)phenyl]ethyl}-1H-indole-2-carboxamide × 1 OLA OLEIC ACID × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；pH 6；293 K；33% PEG 400, 100mM Sodium Cacodylate pH 6.0, 100mM Sodium Malonate Resolution 3.25 Å R-free 0.312

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6KQI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BFW Structure of the C domain of glycogen synthase from Pyrococcus abyssi Deposited 2004-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 218-413
Not recorded SO4 SULFATE ION × 4 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；30% PEG8K, 0.1 M NAAC PH 4.5, 0.2M LITHIUM SULPHATE
Resolution 1.80 Å R-free 0.235
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–437（437 aa）
Not recorded GLC alpha-D-glucopyranose × 1 DIO 1,4-DIETHYLENE DIOXIDE × 4 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.80 Å R-free 0.266
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–437（437 aa）
Not recorded DIO 1,4-DIETHYLENE DIOXIDE × 3 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.80 Å R-free 0.266
2BIS Structure of glycogen synthase from Pyrococcus abyssi Deposited 2005-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–437（437 aa）
Not recorded GLC alpha-D-glucopyranose × 1 DIO 1,4-DIETHYLENE DIOXIDE × 3 GOL GLYCEROL × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.60
Resolution 2.80 Å R-free 0.266
3FRO Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations Deposited 2009-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–437（437 aa）
Chain B 1–437（437 aa）
Chain C 1–437（437 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 PO4 PHOSPHATE ION × 3 NHF 1,5-anhydro-D-fructose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；26-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.255
3L01 Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi Deposited 2009-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–426（426 aa） Fragment：UNP residues 1-426
Mutation：T426A K POTASSIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.228
3L01 Crystal structure of monomeric glycogen synthase from Pyrococcus abyssi Deposited 2009-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–426（426 aa） Fragment：UNP residues 1-426
Mutation：T426A K POTASSIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.228
4S0V Crystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant Deposited 2015-01-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：UNP O43614 residues 3-254, 294-388, and UNP Q9V2J8 residues 218-413
Not recorded SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 OLA OLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions Lipidic Cubic Phase (LCP)；pH 5.9；293 K；31% PEG 400, 0.1 M sodium citrate, 0.2 M sodium formate, 3%(w/v) hexanediol, pH 5.9, Lipidic Cubic Phase (LCP), temperature 293K
Resolution 2.50 Å R-free 0.242
4ZJ8 Structures of the human OX1 orexin receptor bound to selective and dual antagonists Deposited 2015-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：UNP O43613 residues 1-245,UNP Q9V2J8 residues 218-413,UNP O43613 residues 288-380
Not recorded SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 OLA OLEIC ACID × 6 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.4；293 K；100mM Sodium Citrate pH 5.4, 31% PEG 400, 200 mM Sodium Formate
Resolution 2.75 Å R-free 0.273
4ZJC Structures of the human OX1 orexin receptor bound to selective and dual antagonists Deposited 2015-04-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：UNP O43613 residues 1-245,UNP Q9V2J8 residues 218-413,UNP O43613 residues 288-380
Not recorded 4OT [5-(2-fluorophenyl)-2-methyl-1,3-thiazol-4-yl]{(2S)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyrrolidin-1-yl}methanone × 1 OLA OLEIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.6；293 K；100 mM Sodium Citrate pH 5.6, 32% PEG 400, 200 mM Potossium
Resolution 2.83 Å R-free 0.262
5U09 High-resolution crystal structure of the human CB1 cannabinoid receptor Deposited 2016-11-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：P21554 residues 90-301, 333-421 and Q9V2J8 residues 218-413
Mutation：T210A PEG DI(HYDROXYETHYL)ETHER × 9 SO4 SULFATE ION × 4 7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 5.5；293 K；31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate
Resolution 2.60 Å R-free 0.238
5WQC Crystal structure of human orexin 2 receptor bound to the selective antagonist EMPA determined by the synchrotron light source at SPring-8. Deposited 2016-11-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：UNP residues 3-254,UNP residues 218-413,UNP residues 294-386
Not recorded 7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 OLA OLEIC ACID × 5 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；50 mM MES-NaOH (pH 5.8-6.2), 26-29% PEG300, 100 mM sodium malonate, 0.5 mM EMPA, 5% DMSO
Resolution 1.96 Å R-free 0.215
5WS3 Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA Deposited 2016-12-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：UNP residues 3-254,UNP residues 218-413,UNP residues 294-388
Not recorded 7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 OLA OLEIC ACID × 4 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；0.1M MES, 0.1M sodium malonate, 27-30% PEG 300, pH 6.0
Resolution 2.30 Å R-free 0.219
6E59 Crystal structure of the human NK1 tachykinin receptor Deposited 2018-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa） Fragment：receptor (UNP residues 1-227, 238-346) with intervening glycogen synthase (UNP residues 218-413)
Not recorded L76 1-(4-{[(2R,3S)-2-{(1R)-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy}-3-(4-fluorophenyl)morpholin-4-yl]methyl}-1H-1,2,3-triazol-5-yl)-N,N-dimethylmethanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM sodium citrate, pH 5.4, 30% PEG300, 200 mM potassium nitrate, 2% 2,5-hexanediol
Resolution 3.40 Å R-free 0.305
6FJ3 High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist. Deposited 2018-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 218–413（196 aa）
Mutation：;Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A,Y191C, K240M, L300A, M312K, V334I, K359N, L407A, A426L, Q440R, I458A ; Non-standard monomer：Yes (specific site not provided by mmCIF) MAN alpha-D-mannopyranose × 3 OLA OLEIC ACID × 9 ACY ACETIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；0.1 M sodium citrate pH 6.0, 0.3 M sodium acetate, 31% PEG400, 20 uM E-PTH(1-34)
Resolution 2.50 Å R-free 0.248
6HLL Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist CP-99,994 Deposited 2018-09-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 220–413（194 aa）
Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ; GBK (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM MES pH 6.0, 31% (v/v) PEG400, 190-210 mM potassium acetate, 2.4% (v/v) 2,5-hexanediol and 50 uM CP-99,994
Resolution 3.27 Å R-free 0.275
6HLO Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Aprepitant Deposited 2018-09-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 220–413（194 aa）
Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ; Non-standard monomer：Yes (specific site not provided by mmCIF) GBQ 5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one × 1 CIT CITRIC ACID × 1 OLA OLEIC ACID × 17 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 3 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 50-70 mM MgCl2 and 50 uM aprepitant
Resolution 2.40 Å R-free 0.229
6HLP Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist Netupitant Deposited 2018-09-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 220–413（194 aa）
Mutation：;L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A,L74A; V116I; A144L; M181K; A215L; W224R; K243A ; Non-standard monomer：Yes (specific site not provided by mmCIF) GAW 2-[3,5-bis(trifluoromethyl)phenyl]-~{N},2-dimethyl-~{N}-[4-(2-methylphenyl)-6-(4-methylpiperazin-1-yl)pyridin-3-yl]propanamide × 1 CIT CITRIC ACID × 1 OLA OLEIC ACID × 9 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 7 PEG DI(HYDROXYETHYL)ETHER × 24 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；100 mM sodium citrate pH 6.0, 31% (v/v) PEG400, 40-50 mM Mg(HCO2)2 and 50 uM netupitant
Resolution 2.20 Å R-free 0.225
6KP6 The structural study of mutation induced inactivation of Human muscarinic receptor M4 Deposited 2019-08-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：I93T G150A I187A S219Y N449R T459E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.8；293.15 K；300 mM diammonium hydrogen phosphate, 22-26% PEG 300, 0.1M HEPES sodium pH 7.6-8.2
Resolution 3.00 Å R-free 0.264
6LFL Crystal structure of a class A GPCR Deposited 2019-12-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：L135W, A249E, G303A EBX 4-[[3,4-bis(oxidanylidene)-2-[[(1~{R})-1-(4-propan-2-ylfuran-2-yl)propyl]amino]cyclobuten-1-yl]amino]-~{N},~{N}-dimethyl-3-oxidanyl-pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM HEPES pH7.0, 32% PEG 400, 50-150 mM Sodium tartrate dibasic dihydrate salt
Resolution 3.20 Å R-free 0.264
6ME2 XFEL crystal structure of human melatonin receptor MT1 in complex with ramelteon Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) JEV N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide × 1 OLA OLEIC ACID × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol
Resolution 2.80 Å R-free 0.228
6ME3 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-phenylmelatonin Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 OLA OLEIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol
Resolution 2.90 Å R-free 0.229
6ME4 XFEL crystal structure of human melatonin receptor MT1 in complex with 2-iodomelatonin Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ML2 N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol
Resolution 3.20 Å R-free 0.249
6ME5 XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine Deposited 2018-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) AWY ~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide × 1 OLA OLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol
Resolution 3.20 Å R-free 0.257
6PS8 XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin. Deposited 2019-07-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) JEY N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；60-100 mM potassium phosphate monobasic, 100 mM HEPES pH 7.0, 32-35% PEG 400, 1 mM of target ligand 2-phenylmelatonin, 2.5% DMSO, 1.5% propan-2-ol.
Resolution 3.30 Å R-free 0.307
6TPG Crystal structure of the Orexin-2 receptor in complex with EMPA at 2.74 A resolution Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF) 7MA N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide × 1 PG4 TETRAETHYLENE GLYCOL × 1 OLA OLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM trisodium citrate buffer 150-300 mM sodium chloride 28-43 % (v/v) polyethylene glycol 400
Resolution 2.74 Å R-free 0.275
6TPJ Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 13 SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 NH4 AMMONIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) 150-300 mM ammonium nitrate 28-43 % (v/v) polyethylene glycol 400
Resolution 2.74 Å R-free 0.254
6TPJ Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 218–413（196 aa）
Mutation：E54A Y91L D100A V142A R170L L206A Y219A M233A A242L L310V L318A T347A N14D N22D N202D C381W C382W C383W Non-standard monomer：Yes (specific site not provided by mmCIF) OLA OLEIC ACID × 21 SUV [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 NH4 AMMONIUM ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) 150-300 mM ammonium nitrate 28-43 % (v/v) polyethylene glycol 400
Resolution 2.74 Å R-free 0.254
6TPN Crystal structure of the Orexin-2 receptor in complex with HTL6641 at 2.61 A resolution Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NU8 2-(5,6-dimethoxypyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one × 1 NO3 NITRATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 OLA OLEIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100 mM trisodium citrate buffer 150-300 mM lithium nitrate or 150-300 mM potassium nitrate 28-43 % (v/v) polyethylene glycol 400
Resolution 2.61 Å R-free 0.251
6V9S Structure-based development of subtype-selective orexin 1 receptor antagonists Deposited 2019-12-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Not recorded JHC [(2S)-2-[(2S)-butan-2-yl]-4-(5-chloro-1,3-benzoxazol-2-yl)-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl)phenyl]methanone × 1 CLR CHOLESTEROL × 1 OLA OLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM Sodium Citrate pH 5.3, 31% PEG 400, 200 mM Ammonium Formate
Resolution 3.50 Å R-free 0.273
6W25 Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119 Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 218–413（196 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 OLA OLEIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.9；293 K；19% PEG 400, 100 mM Bis-tris propane buffer, and 50 mM CaCl2 2H2O
Resolution 2.75 Å R-free 0.259
7BR3 Crystal structure of the protein 1 Deposited 2020-03-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：P128K 1QW (2R)-2,3-dihydroxypropyl dodecanoate × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 PEG DI(HYDROXYETHYL)ETHER × 6 FMT FORMIC ACID × 1 F5O 4-[[(1R)-2-[5-(2-fluoranyl-3-methoxy-phenyl)-3-[[2-fluoranyl-6-(trifluoromethyl)phenyl]methyl]-4-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]-1-phenyl-ethyl]amino]butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293.15 K；100 mM Na cacodyalte pH 6.0-6.5, 30%-38% PEG400, 150-350 mM NH4NO3
Resolution 2.79 Å R-free 0.284
7FEE Crystal structure of the allosteric modulator ZCZ011 binding to CP55940-bound cannabinoid receptor 1 Deposited 2021-07-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：S203K,T210A,E273K,T283V,R340E,N393D CLR CHOLESTEROL × 2 9GF 2-[(1R,2R,5R)-5-hydroxy-2-(3-hydroxypropyl)cyclohexyl]-5-(2-methyloctan-2-yl)phenol × 1 7IC 6-methyl-3-[(1S)-2-nitro-1-thiophen-2-yl-ethyl]-2-phenyl-1H-indole × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 4 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 2 OLA OLEIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6；293 K；25-36% PEG 300, 100Mm MES pH 6.0, 120-190mM Magnesium Sulfate
Resolution 2.70 Å R-free 0.319
7W41 Crystal Structure of Human Gastrin Releasing Peptide Receptor in complex with the antagonist PD176252 Deposited 2021-11-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Mutation：S127K,I157A,R259E 8B8 (2S)-3-(1H-indol-3-yl)-N-[[1-(5-methoxypyridin-2-yl)cyclohexyl]methyl]-2-methyl-2-[(4-nitrophenyl)carbamoylamino]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.8；294 K；100mM MES, pH 6.8, 300mM Ammonium dihydrogen phosphate, 28% PEG 400, 5% polypropylene glycol P 400
Resolution 2.95 Å R-free 0.321
8CXO Cryo-EM structure of the unliganded mSMO-PGS2 in a lipidic environment Deposited 2022-05-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Not recorded CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JHQ Cryo-EM structure of human S1P transporter SPNS2 bound with S1P Deposited 2023-05-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 218–413（196 aa）
Not recorded S1P (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8KIG Cryo-EM structure of MC3R in complex with SHU9119 Deposited 2023-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 218–413（196 aa）
Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9B9Y Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 218–413（196 aa）
Not recorded 7DY N-[(2S,3S)-4-(4-chlorophenyl)-3-(3-cyanophenyl)butan-2-yl]-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]oxy}propanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9B9Z Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 218–413（196 aa）
Not recorded A1AKO (4S)-3-(4-chlorophenyl)-N'-[(1E)-ethanimidoyl]-4-phenyl-N-[4-(trifluoromethyl)benzene-1-sulfonyl]-4,5-dihydro-1H-pyrazole-1-carboximidamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9BA0 Structural mechanism of CB1R binding to peripheral and biased inverse agonists Deposited 2024-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 218–413（196 aa）
Not recorded A1AKN N-(N-{(E)-[(4S)-3-(4-chlorophenyl)-4-phenyl-4,5-dihydro-1H-pyrazol-1-yl][4-(trifluoromethyl)benzene-1-sulfonamido]methylidene}carbamimidoyl)acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9M88 PGS fused GPR3 dimer with antagonist AF64394 Deposited 2025-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 218–413（196 aa）
Chain D 218–413（196 aa）
Not recorded 5YM (Z)-N-(2-hydroxyethyl)octadec-9-enamide × 2 A1EM1 tetracosan-1-ol × 2 1DO 1-DODECANOL × 8 A1EM3 [(2R)-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-decanoyloxy-propyl] dodecanoate × 4 A1EQ8 icosan-1-ol × 4 A1EM2 N-[(4-chloranyl-2-propan-2-yloxy-phenyl)methyl]-5-phenyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM NaCl, 100mM Hepes, 0.003% LMNG, 0.001% GDN
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

37 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9V2J8_PYRAB
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 210–405； UniProt 218–413

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6kqi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kqi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6kqi
Deposition date deposition_date2019-08-17
Structure title titleStructure of an allosteric modulator bound to the CB1 cannabinoid receptor
Keywords keywordshelix, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.21 Å
Radius of gyration Rg (electron density) rg_electron30.77 Å
Forward intensity I(0) i039027600.00
Molecular weight molecular_weight54427.0 kDa
Excluded volume excluded_volume70543 ų
Envelope volume envelope_volume89269 ų
Hydration-shell volume shell_volume26255 ų
Envelope diameter envelope_diameter108.0 Å
Shell Rg shell_rg35.01 Å
Envelope Rg envelope_rg30.66 Å
Shape Rg shape_rg30.76 Å
Total Rg total_rg31.27 Å
Total atoms total_atoms3828
Residues n_residues473
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.6 Å
Rg (real space) rg_real31.59 Å
Rg uncertainty (real space) rg_real_error1.03 Å
I(0) (real space) i0_real3.9030e+07
I(0) uncertainty (real space) i0_real_error6.7890e+05
Rg (reciprocal space) rg_reciprocal31.43 Å
I(0) (reciprocal space) i0_reciprocal39020000.0000
Solution quality estimate total_estimate0.7802
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary24.6 Å
Skewness Skewness skewness0.487
Kurtosis Kurtosis kurtosis-0.628
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14060000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.615; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.443; Smooth: 0.849
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id6kqiA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2000 — Glycogen Phosphorylase B;
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8. Citations (1)

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9. Files and Curves (10)