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

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Ligand Amino Acid Generic Number Segment Interaction Type
agomelatine A104 3.29x29 TM3 Van der Waals
agomelatine M107 3.32x32 TM3 hydrophobic
agomelatine G108 3.33x33 TM3 Van der Waals
agomelatine V111 3.36x36 TM3 Van der Waals
agomelatine I112 3.37x37 TM3 Van der Waals
agomelatine V159 4.57x57 TM4 hydrophobic
agomelatine N162 4.60x61 TM4 Van der Waals
agomelatine L168 ECL2 hydrophobic
agomelatine T178 45.51x51 ECL2 Van der Waals
agomelatine F179 45.52x52 ECL2 hydrophobic
agomelatine Q181 ECL2 polar (hydrogen bond)
agomelatine V191 5.42x43 TM5 hydrophobic
agomelatine V192 5.43x44 TM5 hydrophobic
agomelatine L254 6.51x51 TM6 Van der Waals
agomelatine N255 6.52x52 TM6 Van der Waals

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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
3x29 3.29x29 G104
3x32 3.32x32 M107
3x33 3.33x33 G108
3x36 3.36x36 V111
3x37 3.37x37 I112
TM4
4x57 4.57x57 V159
4x61 4.60x61 N162
ECL2
45x51 45.51x51 T178
45x52 45.52x52 F179
TM5
5x43 5.42x43 V191
5x44 5.43x44 V192
TM6
6x51 6.51x51 L254
6x52 6.52x52 N255