PDB
7C61
Resolution
3.0 Å
Released
July 29, 2020
Receptor
5-HT1B
Class
A
Species
Homo sapiens
Ligand
Function
ergotamine
Agonist
Reference
10.1038/S41598-020-68355-X

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Ligand Amino Acid Generic Number Segment Interaction Type
ergotamine Y109 2.64x63 TM2 Van der Waals
ergotamine W125 3.28x28 TM3 hydrophobic
ergotamine L126 3.29x29 TM3 Van der Waals
ergotamine D129 3.32x32 TM3 polar (hydrogen bond)
ergotamine D129 3.32x32 TM3 polar (charge-charge)
ergotamine I130 3.33x33 TM3 hydrophobic
ergotamine C133 3.36x36 TM3 hydrophobic
ergotamine T134 3.37x37 TM3 Van der Waals
ergotamine C199 45.50x50 ECL2 Van der Waals
ergotamine V200 45.51x51 ECL2 Van der Waals
ergotamine V201 45.52x52 ECL2 hydrophobic
ergotamine T203 ECL2 Van der Waals
ergotamine S212 5.42x43 TM5 Van der Waals
ergotamine A216 5.46x461 TM5 Van der Waals
ergotamine W367 6.48x48 TM6 hydrophobic
ergotamine F370 6.51x51 TM6 aromatic (edge-to-face)
ergotamine F370 6.51x51 TM6 hydrophobic
ergotamine F371 6.52x52 TM6 aromatic (edge-to-face)
ergotamine S374 6.55x55 TM6 Van der Waals
ergotamine L388 7.32x31 TM7 Van der Waals
ergotamine F391 7.35x34 TM7 hydrophobic
ergotamine D392 7.36x35 TM7 Van der Waals
ergotamine T395 7.39x38 TM7 Van der Waals
ergotamine Y399 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
5-HT1B receptor
TM2
2x63 2.64x63 Y109
TM3
3x28 3.28x28 W125
3x29 3.29x29 L126
3x32 3.32x32 D129
3x33 3.33x33 I130
3x36 3.36x36 C133
3x37 3.37x37 T134
ECL2
45x50 45.50x50 C199
45x51 45.51x51 V200
45x52 45.52x52 V201
TM5
5x43 5.42x43 S212
5x461 5.46x461 A216
TM6
6x48 6.48x48 W327
6x51 6.51x51 F330
6x52 6.52x52 F331
6x55 6.55x55 S334
TM7
7x31 7.32x31 L348
7x34 7.35x34 F351
7x35 7.36x35 D352
7x38 7.39x38 T355
7x42 7.43x42 Y359