PDB
8XQF
Resolution
3.1 Å
Released
Jan. 22, 2025
Receptor
apelin
Class
A
Species
Homo sapiens
Ligand
Function
apelin-13 (Human)
Agonist
Reference
10.1038/S41467-024-55555-6

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Ligand Amino Acid Generic Number Segment Interaction Type
apelin-13 (Human) E20 N-term Van der Waals
apelin-13 (Human) T22 N-term Van der Waals
apelin-13 (Human) Y35 1.39x39 TM1 Van der Waals
apelin-13 (Human) F78 2.53x53 TM2 Van der Waals
apelin-13 (Human) W85 2.60x60 TM2 hydrophobic
apelin-13 (Human) Y88 2.63x63 TM2 polar (hydrogen bond)
apelin-13 (Human) T89 2.64x64 TM2 Van der Waals
apelin-13 (Human) Y93 ECL1 hydrophobic
apelin-13 (Human) I109 3.32x32 TM3 hydrophobic
apelin-13 (Human) F110 3.33x33 TM3 hydrophobic
apelin-13 (Human) M113 3.36x36 TM3 Van der Waals
apelin-13 (Human) V164 4.60x61 TM4 hydrophobic
apelin-13 (Human) L167 4.63x64 TM4 Van der Waals
apelin-13 (Human) R168 ECL2 Van der Waals
apelin-13 (Human) E174 ECL2 Van der Waals
apelin-13 (Human) Q180 ECL2 Van der Waals
apelin-13 (Human) Y182 45.51x51 ECL2 Van der Waals
apelin-13 (Human) M183 45.52x52 ECL2 hydrophobic
apelin-13 (Human) M183 45.52x52 ECL2 polar (hydrogen bond with backbone)
apelin-13 (Human) Y185 ECL2 Van der Waals
apelin-13 (Human) E194 5.31x32 TM5 polar (hydrogen bond)
apelin-13 (Human) E194 5.31x32 TM5 polar (charge-charge)
apelin-13 (Human) E198 5.35x36 TM5 polar (charge-charge)
apelin-13 (Human) E198 5.35x36 TM5 polar (hydrogen bond)
apelin-13 (Human) L201 5.38x39 TM5 hydrophobic
apelin-13 (Human) G202 5.39x40 TM5 Van der Waals
apelin-13 (Human) S205 5.42x43 TM5 Van der Waals
apelin-13 (Human) Y264 6.51x51 TM6 Van der Waals
apelin-13 (Human) K268 6.55x55 TM6 polar (charge-charge)
apelin-13 (Human) K268 6.55x55 TM6 polar (hydrogen bond)
apelin-13 (Human) Y271 6.58x58 TM6 polar (hydrogen bond)
apelin-13 (Human) Y271 6.58x58 TM6 hydrophobic
apelin-13 (Human) S275 6.62x62 TM6 Van der Waals
apelin-13 (Human) F291 7.35x34 TM7 Van der Waals
apelin-13 (Human) T295 7.39x38 TM7 hydrophobic
apelin-13 (Human) Y299 7.43x42 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
TM1
1x39 1.39x39 Y35
TM2
2x53 2.53x53 F78
2x60 2.60x60 W85
2x63 2.63x63 Y88
2x64 2.64x64 T89
TM3
3x32 3.32x32 I109
3x33 3.33x33 F110
3x36 3.36x36 M113
TM4
4x61 4.60x61 V164
4x64 4.63x64 L167
ECL2
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
5x43 5.42x43 S205
TM6
6x51 6.51x51 Y264
6x55 6.55x55 K268
6x58 6.58x58 Y271
6x62 6.62x62 S275
TM7
7x34 7.35x34 F291
7x38 7.39x38 T295
7x42 7.43x42 Y299