PDB
7F9Y
Resolution
2.9 Å
Released
Aug. 18, 2021
Receptor
ghrelin
Class
A
Species
Homo sapiens
Ligands
Ghrelin
OCTANOIC ACID
Function
Agonist
Agonist
Reference
10.1038/S41467-021-25364-2
Ghrelin OCTANOIC ACID

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Ligand Amino Acid Generic Number Segment Interaction Type
Ghrelin L37 N-term hydrophobic
Ghrelin F38 N-term hydrophobic
Ghrelin R102 2.63x63 TM2 polar (charge-assisted hydrogen bond)
Ghrelin Y106 2.67x67 TM2 Van der Waals
Ghrelin Y106 2.67x67 TM2 polar (hydrogen bond)
OCTANOIC ACID Q120 3.29x29 TM3 polar (hydrogen bond)
Ghrelin Q120 3.29x29 TM3 polar (hydrogen bond)
Ghrelin Q120 3.29x29 TM3 polar (hydrogen bond)
OCTANOIC ACID Q120 3.29x29 TM3 Van der Waals
Ghrelin S123 3.32x32 TM3 Van der Waals
OCTANOIC ACID E124 3.33x33 TM3 Van der Waals
Ghrelin E124 3.33x33 TM3 Van der Waals
OCTANOIC ACID Y128 3.37x37 TM3 Van der Waals
Ghrelin Y128 3.37x37 TM3 Van der Waals
Ghrelin I178 4.60x61 TM4 hydrophobic
OCTANOIC ACID I178 4.60x61 TM4 hydrophobic
Ghrelin I178 4.60x61 TM4 Van der Waals
OCTANOIC ACID I178 4.60x61 TM4 Van der Waals
Ghrelin E197 ECL2 polar (charge-assisted hydrogen bond)
OCTANOIC ACID V212 5.38x38 TM5 Van der Waals
Ghrelin V212 5.38x38 TM5 Van der Waals
OCTANOIC ACID M213 5.39x39 TM5 Van der Waals
OCTANOIC ACID M213 5.39x39 TM5 hydrophobic
Ghrelin M213 5.39x39 TM5 Van der Waals
Ghrelin M213 5.39x39 TM5 hydrophobic
OCTANOIC ACID R283 6.55x55 TM6 Van der Waals
Ghrelin R283 6.55x55 TM6 Van der Waals
Ghrelin F286 6.58x58 TM6 hydrophobic
Ghrelin F286 6.58x58 TM6 Van der Waals
Ghrelin S289 6.61x61 TM6 Van der Waals
Ghrelin F290 6.62x62 TM6 Van der Waals
Ghrelin F290 6.62x62 TM6 hydrophobic
Ghrelin A298 7.28x27 TM7 hydrophobic
Ghrelin A298 7.28x27 TM7 Van der Waals
Ghrelin Q299 7.29x28 TM7 polar (hydrogen bond)
Ghrelin Q302 7.32x31 TM7 polar (hydrogen bond)
Ghrelin Q302 7.32x31 TM7 polar (hydrogen bond)
Ghrelin N305 7.35x34 TM7 Van der Waals
Ghrelin N305 7.35x34 TM7 polar (hydrogen bond)
Ghrelin F309 7.39x38 TM7 hydrophobic
Ghrelin F309 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
ghrelin receptor
TM2
2x63 2.63x63 R102
2x67 2.67x67 Y106
TM3
3x29 3.29x29 Q120
3x32 3.32x32 S123
3x33 3.33x33 E124
3x37 3.37x37 Y128
TM4
4x61 4.60x61 I178
TM5
5x38 5.38x38 V212
5x39 5.39x39 M213
TM6
6x55 6.55x55 R283
6x58 6.58x58 F286
6x61 6.61x61 S289
6x62 6.62x62 F290
TM7
7x27 7.28x27 A298
7x28 7.29x28 Q299
7x31 7.32x31 Q302
7x34 7.35x34 N305
7x38 7.39x38 F309