PDB
9EK0
Resolution
2.8 Å
Released
Oct. 8, 2025
Receptor
M5
Class
A
Species
Homo sapiens
Ligand
Function
iperoxo
Agonist
Reference
10.1038/S41467-025-62212-Z

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Ligand Amino Acid Generic Number Segment Interaction Type
iperoxo D110 3.32x32 TM3 polar (charge-charge)
iperoxo Y111 3.33x33 TM3 aromatic (pi-cation)
iperoxo Y111 3.33x33 TM3 hydrophobic
iperoxo S114 3.36x36 TM3 Van der Waals
iperoxo N115 3.37x37 TM3 Van der Waals
iperoxo V118 3.40x40 TM3 hydrophobic
iperoxo W162 4.57x57 TM4 Van der Waals
iperoxo A201 5.46x461 TM5 hydrophobic
iperoxo F202 5.47x47 TM5 Van der Waals
iperoxo W455 6.48x48 TM6 hydrophobic
iperoxo Y458 6.51x51 TM6 hydrophobic
iperoxo Y458 6.51x51 TM6 aromatic (pi-cation)
iperoxo N459 6.52x52 TM6 Van der Waals
iperoxo Y481 7.39x38 TM7 aromatic (pi-cation)
iperoxo C484 7.42x41 TM7 Van der Waals
iperoxo Y485 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
M5 receptor
TM3
3x32 3.32x32 D110
3x33 3.33x33 Y111
3x36 3.36x36 S114
3x37 3.37x37 N115
3x40 3.40x40 V118
TM4
4x57 4.57x57 W162
TM5
5x461 5.46x461 A201
5x47 5.47x47 F202
TM6
6x48 6.48x48 W455
6x51 6.51x51 Y458
6x52 6.52x52 N459
TM7
7x38 7.39x38 Y481
7x41 7.42x41 C484
7x42 7.43x42 Y485