PDB
9N29
Resolution
2.6 Å
Released
July 15, 2026
Receptor
M4
Class
A
Species
Homo sapiens
Ligand
diphenhydramine
Function
Agonist
Reference
10.1038/S41392-026-02865-4

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Ligand Amino Acid Generic Number Segment Interaction Type
diphenhydramine D112 3.32x32 TM3 polar (charge-assisted hydrogen bond)
diphenhydramine C113 3.33x33 TM3 Van der Waals
diphenhydramine S116 3.36x36 TM3 Van der Waals
diphenhydramine N117 3.37x37 TM3 Van der Waals
diphenhydramine W164 4.57x57 TM4 aromatic (face-to-face)
diphenhydramine W164 4.57x57 TM4 Van der Waals
diphenhydramine F189 ECL2 hydrophobic
diphenhydramine A200 5.43x44 TM5 hydrophobic
diphenhydramine G203 5.46x461 TM5 Van der Waals
diphenhydramine F204 5.47x47 TM5 Van der Waals
diphenhydramine F204 5.47x47 TM5 hydrophobic
diphenhydramine W413 6.48x48 TM6 aromatic (edge-to-face)
diphenhydramine W413 6.48x48 TM6 Van der Waals
diphenhydramine F416 6.51x51 TM6 hydrophobic
diphenhydramine F416 6.51x51 TM6 Van der Waals
diphenhydramine N417 6.52x52 TM6 Van der Waals
diphenhydramine V420 6.55x55 TM6 hydrophobic
diphenhydramine V420 6.55x55 TM6 Van der Waals
diphenhydramine Y439 7.39x38 TM7 hydrophobic
diphenhydramine Y439 7.39x38 TM7 Van der Waals
diphenhydramine C442 7.42x41 TM7 Van der Waals
diphenhydramine Y443 7.43x42 TM7 Van der Waals
diphenhydramine Y443 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
M4 receptor
TM3
3x32 3.32x32 D112
3x33 3.33x33 Y113
3x36 3.36x36 S116
3x37 3.37x37 N117
TM4
4x57 4.57x57 W164
TM5
5x44 5.43x44 A200
5x461 5.46x461 A203
5x47 5.47x47 F204
TM6
6x48 6.48x48 W413
6x51 6.51x51 Y416
6x52 6.52x52 N417
6x55 6.55x55 V420
TM7
7x38 7.39x38 Y439
7x41 7.42x41 C442
7x42 7.43x42 Y443