PDB
6DS0
Resolution
3.2 Å
Released
Aug. 29, 2018
Receptor
5-HT2B
Class
A
Species
Homo sapiens
Ligand
Function
LY266097
Agonist (partial)
Reference
10.1038/s41594-018-0116-7

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Ligand Amino Acid Generic Number Segment Interaction Type
LY266097 A111 2.61x60 TM2 Van der Waals
LY266097 T114 2.64x63 TM2 Van der Waals
LY266097 W131 3.28x28 TM3 hydrophobic
LY266097 D135 3.32x32 TM3 polar (hydrogen bond)
LY266097 D135 3.32x32 TM3 polar (charge-charge)
LY266097 V136 3.33x33 TM3 hydrophobic
LY266097 S139 3.36x36 TM3 Van der Waals
LY266097 I186 4.56x56 TM4 Van der Waals
LY266097 V208 45.51x51 ECL2 Van der Waals
LY266097 L209 45.52x52 ECL2 hydrophobic
LY266097 F217 5.38x39 TM5 hydrophobic
LY266097 M218 5.39x40 TM5 Van der Waals
LY266097 G221 5.42x43 TM5 Van der Waals
LY266097 S222 5.43x44 TM5 Van der Waals
LY266097 A225 5.46x461 TM5 hydrophobic
LY266097 W337 6.48x48 TM6 Van der Waals
LY266097 F340 6.51x51 TM6 hydrophobic
LY266097 F340 6.51x51 TM6 aromatic (edge-to-face)
LY266097 F341 6.52x52 TM6 hydrophobic
LY266097 N344 6.55x55 TM6 Van der Waals
LY266097 L362 7.35x34 TM7 Van der Waals
LY266097 E363 7.36x35 TM7 Van der Waals
LY266097 V366 7.39x38 TM7 hydrophobic
LY266097 Y370 7.43x42 TM7 Van der Waals

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Snake plot — Download: PNG | SVG
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
2x63 2.64x63 T114
TM3
3x28 3.28x28 W131
3x32 3.32x32 D135
3x33 3.33x33 V136
3x36 3.36x36 S139
TM4
4x56 4.56x56 I186
ECL2
45x51 45.51x51 V208
45x52 45.52x52 L209
TM5
5x39 5.38x39 F217
5x40 5.39x40 M218
5x43 5.42x43 G221
5x44 5.43x44 S222
5x461 5.46x461 A225
TM6
6x48 6.48x48 W337
6x51 6.51x51 F340
6x52 6.52x52 F341
6x55 6.55x55 N344
TM7
7x34 7.35x34 L362
7x35 7.36x35 E363
7x38 7.39x38 V366
7x42 7.43x42 Y370