PDB
8Z74
Resolution
3.0 Å
Released
Jan. 22, 2025
Receptor
apelin
Class
A
Species
Homo sapiens
Ligand
JN241-9
Function
Agonist
Reference
10.1038/S41467-024-55555-6

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Ligand Amino Acid Generic Number Segment Interaction Type
JN241-9 Y93 ECL1 aromatic (face-to-face)
JN241-9 F110 3.33x33 TM3 hydrophobic
JN241-9 L173 ECL2 hydrophobic
JN241-9 E174 ECL2 polar (charge-assisted hydrogen bond)
JN241-9 E174 ECL2 polar (hydrogen bond with backbone)
JN241-9 N175 ECL2 Van der Waals
JN241-9 T176 ECL2 Van der Waals
JN241-9 Q180 ECL2 Van der Waals
JN241-9 C181 45.50x50 ECL2 polar (hydrogen bond with backbone)
JN241-9 C181 45.50x50 ECL2 Van der Waals
JN241-9 Y182 45.51x51 ECL2 polar (hydrogen bond)
JN241-9 M183 45.52x52 ECL2 Van der Waals
JN241-9 M183 45.52x52 ECL2 hydrophobic
JN241-9 V191 5.28x29 TM5 Van der Waals
JN241-9 V191 5.28x29 TM5 hydrophobic
JN241-9 E194 5.31x32 TM5 polar (charge-assisted hydrogen bond)
JN241-9 E198 5.35x36 TM5 polar (charge-assisted hydrogen bond)
JN241-9 L201 5.38x39 TM5 Van der Waals
JN241-9 G202 5.39x40 TM5 Van der Waals
JN241-9 Y264 6.51x51 TM6 Van der Waals
JN241-9 Y264 6.51x51 TM6 hydrophobic
JN241-9 V267 6.54x54 TM6 Van der Waals
JN241-9 K268 6.55x55 TM6 polar (charge-assisted hydrogen bond)
JN241-9 Y271 6.58x58 TM6 Van der Waals
JN241-9 Y271 6.58x58 TM6 polar (hydrogen bond)
JN241-9 C281 7.25x24 TM7 Van der Waals
JN241-9 C281 7.25x24 TM7 hydrophobic
JN241-9 D284 7.28x27 TM7 Van der Waals
JN241-9 L285 7.29x28 TM7 Van der Waals
JN241-9 M288 7.32x31 TM7 Van der Waals
JN241-9 M288 7.32x31 TM7 polar (hydrogen bond with backbone)
JN241-9 N289 7.33x32 TM7 polar (hydrogen bond)
JN241-9 F291 7.35x34 TM7 Van der Waals
JN241-9 F291 7.35x34 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
apelin receptor
TM3
3x33 3.33x33 F110
ECL2
45x50 45.50x50 C181
45x51 45.51x51 Y182
45x52 45.52x52 M183
TM5
5x32 5.31x32 E194
5x36 5.35x36 E198
5x39 5.38x39 L201
5x40 5.39x40 G202
TM6
6x51 6.51x51 Y264
6x54 6.54x54 V267
6x55 6.55x55 K268
6x58 6.58x58 Y271
TM7
7x24 7.25x24 C281
7x27 7.28x27 D284
7x28 7.29x28 L285
7x31 7.32x31 M288
7x32 7.33x32 N289
7x34 7.35x34 F291