PDB
9JMD
Resolution
2.7 Å
Released
May 28, 2025
Receptor
motilin
Class
A
Species
Homo sapiens
Ligand
azithromycin
Function
Agonist
Reference
10.1016/J.CELREP.2025.115329

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Ligand Amino Acid Generic Number Segment Interaction Type
azithromycin D94 2.60x60 TM2 polar (charge-assisted hydrogen bond)
azithromycin R97 2.63x63 TM2 polar (hydrogen bond with backbone)
azithromycin R97 2.63x63 TM2 polar (charge-assisted hydrogen bond)
azithromycin L98 2.64x64 TM2 Van der Waals
azithromycin L98 2.64x64 TM2 hydrophobic
azithromycin S101 ECL1 Van der Waals
azithromycin S101 ECL1 polar (hydrogen bond with backbone)
azithromycin L115 3.29x29 TM3 hydrophobic
azithromycin L115 3.29x29 TM3 Van der Waals
azithromycin G118 3.32x32 TM3 Van der Waals
azithromycin E119 3.33x33 TM3 polar (charge-assisted hydrogen bond)
azithromycin F173 4.60x61 TM4 Van der Waals
azithromycin E234 ECL2 polar (charge-assisted hydrogen bond)
azithromycin C235 45.50x50 ECL2 polar (hydrogen bond with backbone)
azithromycin C235 45.50x50 ECL2 Van der Waals
azithromycin R236 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
azithromycin L249 5.40x41 TM5 Van der Waals
azithromycin F314 6.51x51 TM6 Van der Waals
azithromycin F314 6.51x51 TM6 hydrophobic
azithromycin R318 6.55x55 TM6 polar (charge-assisted hydrogen bond)
azithromycin Y321 6.58x58 TM6 hydrophobic
azithromycin Y321 6.58x58 TM6 Van der Waals
azithromycin Q334 7.32x31 TM7 polar (hydrogen bond)
azithromycin N337 7.35x34 TM7 Van der Waals
azithromycin N337 7.35x34 TM7 polar (hydrogen bond with backbone)
azithromycin I338 7.36x35 TM7 Van der Waals
azithromycin L341 7.39x38 TM7 hydrophobic
azithromycin L341 7.39x38 TM7 Van der Waals
azithromycin F344 7.42x41 TM7 hydrophobic
azithromycin F344 7.42x41 TM7 Van der Waals
azithromycin Y345 7.43x42 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
motilin receptor
TM2
2x60 2.60x60 D94
2x63 2.63x63 R97
2x64 2.64x64 L98
TM3
3x29 3.29x29 L115
3x32 3.32x32 G118
3x33 3.33x33 E119
TM4
4x61 4.60x61 F173
ECL2
45x50 45.50x50 C235
45x51 45.51x51 R236
TM5
5x41 5.40x41 L249
TM6
6x51 6.51x51 F314
6x55 6.55x55 R318
6x58 6.58x58 Y321
TM7
7x31 7.32x31 Q334
7x34 7.35x34 N337
7x35 7.36x35 I338
7x38 7.39x38 L341
7x41 7.42x41 F344
7x42 7.43x42 Y345