PDB
9JGK
Resolution
3.6 Å
Released
July 16, 2025
Receptor
5-HT2B
Class
A
Species
Homo sapiens
Ligand
Function
balovaptan
Antagonist
Reference
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Ligand Amino Acid Generic Number Segment Interaction Type
balovaptan A111 2.61x60 TM2 hydrophobic
balovaptan W131 3.28x28 TM3 Van der Waals
balovaptan D135 3.32x32 TM3 Van der Waals
balovaptan V136 3.33x33 TM3 hydrophobic
balovaptan S139 3.36x36 TM3 Van der Waals
balovaptan T140 3.37x37 TM3 Van der Waals
balovaptan C207 45.50x50 ECL2 Van der Waals
balovaptan V208 45.51x51 ECL2 Van der Waals
balovaptan L209 45.52x52 ECL2 Van der Waals
balovaptan F217 5.38x39 TM5 Van der Waals
balovaptan G221 5.42x43 TM5 Van der Waals
balovaptan S222 5.43x44 TM5 Van der Waals
balovaptan A225 5.46x461 TM5 hydrophobic
balovaptan F419 6.51x51 TM6 hydrophobic
balovaptan E442 7.36x35 TM7 Van der Waals
balovaptan W446 7.40x39 TM7 hydrophobic
balovaptan W446 7.40x39 TM7 aromatic (edge-to-face)
balovaptan Y449 7.43x42 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
5-HT2B receptor
TM2
2x60 2.61x60 A111
TM3
3x28 3.28x28 W131
3x32 3.32x32 D135
3x33 3.33x33 V136
3x36 3.36x36 S139
3x37 3.37x37 T140
ECL2
45x50 45.50x50 C207
45x51 45.51x51 V208
45x52 45.52x52 L209
TM5
5x39 5.38x39 F217
5x43 5.42x43 G221
5x44 5.43x44 S222
5x461 5.46x461 A225
TM6
6x51 6.51x51 F340
TM7
7x35 7.36x35 E363
7x39 7.40x39 W367
7x42 7.43x42 Y370