Structure information

CB2 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

8GUT

SPECIES

Homo sapiens

RESOLUTION

2.980

PREFERRED CHAIN

R

REFERENCE

10.1038/S41467-023-37112-9

PUBLICATION DATE

May 10, 2023

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F87 2.57x57 TM2 aromatic (edge-to-face)
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F94 2.64x64 TM2 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F106 3.25x25 TM3 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione I110 3.29x29 TM3 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione T114 3.33x33 TM3 polar (hydrogen bond)
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione T114 3.33x33 TM3 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F117 3.36x36 TM3 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F117 3.36x36 TM3 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F183 ECL2 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F183 ECL2 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione P184 ECL2 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione P184 ECL2 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione I186 ECL2 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione Y190 5.39x39 TM5 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione L191 5.40x40 TM5 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione W194 5.43x43 TM5 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione W194 5.43x43 TM5 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione W258 6.48x48 TM6 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione W258 6.48x48 TM6 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione M265 6.55x55 TM6 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F281 7.35x34 TM7 Van der Waals
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione F281 7.35x34 TM7 hydrophobic
1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione S285 7.39x38 TM7 Van der Waals

Ligands

1-[[4-[5-Fluoro-6-[(oxan-4-ylamino)methyl]pyridin-2-yl]phenyl]methyl]-3-(2-methylpropyl)imidazolidine-2,4-dione

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Residue Diagrams

V N E L A S L L G L L T C L V A V A T K 1 G S L A G A D F L A S V V F A C S F V N 2 L L L S G V S A T F T M T V S G I K L L 3 A L V T L G I M W V L S A L V S Y L P L 4 Y T Y I I G S F L F A I F L L W S L L Y 5 G L V L A V L L I C W F P V L A L M A H 6 V P N V M S N I L C L M S C F A F A K 7
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ICL1 H Q L R R ICL1ECL1 F H G V D ECL1ICL2 P P S Y K A L L ICL2ECL2 W T C C P R P C S E L F P L I ECL2ICL3 H Q D R Q V P G M A R M ICL3ECL3 T L ECL3N-term M E E C W V T E I A N G S K D G L D S N P M K D Y M I L N-termC-term C V R G L G S E A K E E A P R S S V T E T E A D G K I T P W P D S R D L D L S D C C-term S G P Q K T A V A V L C T L L G L L S A L E N V A V L Y L I L S S K P S Y L F I G S L A G A D F L A S V V F A C S F V N F H V S K A V F L L K I G S V T M T F T A S V G S L L L T A I D R Y L C L R Y T R G R A L V T L G I M W V L S A L V S Y L P L M G P N D Y L L S W L L F I A F L F S G I I Y T Y G H V L W K A H Q H V A S L S G R L D V R L A K T L G L V L A V L L I C W F P V L A L M A H S L A T S D Q V K K A F A F C S M L C L I N S M V N P V I Y A L R S G E A H H W K K I R S S C L A H
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Residue Table


GPCRdb(A)
GPCRdb(A)
CB2 receptor
TM2
2x57 2.57x57 F87
2x64 2.64x64 F94
TM3
3x25 3.25x25 F106
3x29 3.29x29 I110
3x33 3.33x33 T114
3x36 3.36x36 F117
TM5
5x39 5.39x39 Y190
5x40 5.40x40 L191
5x43 5.43x43 W194
TM6
6x48 6.48x48 W258
6x55 6.55x55 M265
TM7
7x34 7.35x34 F281
7x38 7.39x38 S285