PDB
6ME5
Resolution
3.2 Å
Released
April 24, 2019
Receptor
MT1
Class
A
Species
Homo sapiens
Ligand
agomelatine
Function
Agonist
Reference
10.1038/S41586-019-1141-3

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Ligand Amino Acid Generic Number Segment Interaction Type
agomelatine M107 3.32x32 TM3 hydrophobic
agomelatine N162 4.60x61 TM4 polar (hydrogen bond)
agomelatine N162 4.60x61 TM4 Van der Waals
agomelatine T178 45.51x51 ECL2 Van der Waals
agomelatine F179 45.52x52 ECL2 hydrophobic
agomelatine F179 45.52x52 ECL2 Van der Waals
agomelatine Q181 ECL2 polar (hydrogen bond)
agomelatine Q181 ECL2 Van der Waals
agomelatine V191 5.42x43 TM5 Van der Waals
agomelatine V191 5.42x43 TM5 hydrophobic
agomelatine L254 6.51x51 TM6 Van der Waals
agomelatine L254 6.51x51 TM6 hydrophobic

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Snake plot — Download: PNG | SVG
ICL1 K K L R ICL1ECL1 G W N L ECL1ICL2 S L K Y D K L Y ICL2ECL2 T L Q Y D P R I Y S C T F A Q S V ECL2ICL3 K P D R K ICL3ECL3 P A S M V P R I ECL3N-term M Q G N G S A L P N A S Q P V L R G D G A R N-termC-term A R V F F V D S S N D V A D R V K W K P S P L M T N N N V V K V D S V C-term P S W L A S A L A C V L I F T I V V D I L G N L L V I L S V Y R N N A G N I F V V S L A V A D L V V A I Y P Y P L V L M S I F N N G Y L H C Q V S G F L M G L S V I G S I F N I T G I A I N R Y C Y I C H S S K N S L C Y V L L I W L L T L A A V L P N L R A G S S A Y T I A V V V F H F L V P M I I V I F C Y L R I W I L V L Q V R Q R V P K L K P Q D F R N F V T M F V V F V L F A I C W A P L N F I G L A V A S D P E W L F V A S Y Y M A Y F N S C L N A I I Y G L L N Q N Y R R L C T F R K E I I V S
Helix box plot — Download: PNG | SVG L N G L I D V V I T F I L V C A L A S A 1 V S L A V A D L V V A Y I P Y P L V L M S 2 G T I N F I S G I V S L G M L F G S V Q 3 S L C Y V L L I W L L T L A A V L P N 4 Y C F I V I I M P V L F H F V V V A I T Y 5 F V V F V L F A I C W A P L N F I G L A 6 I A N L C S N F Y A M Y Y S A V F L W 7

GPCRdb(A)
GPCRdb(A)
MT1 receptor
TM3
3x32 3.32x32 M107
TM4
4x61 4.60x61 N162
ECL2
45x51 45.51x51 T178
45x52 45.52x52 F179
TM5
5x43 5.42x43 V191
TM6
6x51 6.51x51 L254