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

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Ligand Amino Acid Generic Number Segment Interaction Type
apelin-13 (Human) Y35 1.39x39 TM1 hydrophobic
apelin-13 (Human) W85 2.60x60 TM2 hydrophobic
apelin-13 (Human) T89 2.64x64 TM2 polar (hydrogen bond with backbone)
apelin-13 (Human) T89 2.64x64 TM2 Van der Waals
apelin-13 (Human) Y93 ECL1 hydrophobic
apelin-13 (Human) Y93 ECL1 Van der Waals
apelin-13 (Human) S106 3.29x29 TM3 Van der Waals
apelin-13 (Human) I109 3.32x32 TM3 Van der Waals
apelin-13 (Human) I109 3.32x32 TM3 hydrophobic
apelin-13 (Human) F110 3.33x33 TM3 Van der Waals
apelin-13 (Human) F110 3.33x33 TM3 hydrophobic
apelin-13 (Human) R168 4.64x65 TM4 polar (charge-assisted hydrogen bond)
apelin-13 (Human) E174 ECL2 polar (charge-assisted hydrogen bond)
apelin-13 (Human) Q180 ECL2 Van der Waals
apelin-13 (Human) C181 45.50x50 ECL2 polar (hydrogen bond with backbone)
apelin-13 (Human) C181 45.50x50 ECL2 Van der Waals
apelin-13 (Human) Y182 45.51x51 ECL2 Van der Waals
apelin-13 (Human) M183 45.52x52 ECL2 Van der Waals
apelin-13 (Human) M183 45.52x52 ECL2 polar (hydrogen bond with backbone)
apelin-13 (Human) Y185 ECL2 polar (hydrogen bond)
apelin-13 (Human) Y185 ECL2 Van der Waals
apelin-13 (Human) L201 5.38x39 TM5 Van der Waals
apelin-13 (Human) L201 5.38x39 TM5 hydrophobic
apelin-13 (Human) S205 5.42x43 TM5 Van der Waals
apelin-13 (Human) Y264 6.51x51 TM6 hydrophobic
apelin-13 (Human) Y264 6.51x51 TM6 Van der Waals
apelin-13 (Human) Y271 6.58x58 TM6 Van der Waals
apelin-13 (Human) Y271 6.58x58 TM6 polar (hydrogen bond)
apelin-13 (Human) M288 7.32x31 TM7 Van der Waals
apelin-13 (Human) F291 7.35x34 TM7 hydrophobic
apelin-13 (Human) F291 7.35x34 TM7 Van der Waals
apelin-13 (Human) Y299 7.43x42 TM7 polar (hydrogen bond)

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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
2x60 2.60x60 W85
2x64 2.64x64 T89
TM3
3x29 3.29x29 S106
3x32 3.32x32 I109
3x33 3.33x33 F110
TM4
4x65 4.64x65 R168
ECL2
45x50 45.50x50 C181
45x51 45.51x51 Y182
45x52 45.52x52 M183
TM5
5x39 5.38x39 L201
5x43 5.42x43 S205
TM6
6x51 6.51x51 Y264
6x58 6.58x58 Y271
TM7
7x31 7.32x31 M288
7x34 7.35x34 F291
7x42 7.43x42 Y299