PDB
6G79
Resolution
3.8 Å
Released
June 20, 2018
Receptor
5-HT1B
Class
A
Species
Homo sapiens
Ligand
Function
donitriptan
Agonist
Reference
10.1038/S41586-018-0241-9

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Ligand Amino Acid Generic Number Segment Interaction Type
donitriptan D129 3.32x32 TM3 polar (charge-charge)
donitriptan D129 3.32x32 TM3 polar (hydrogen bond)
donitriptan I130 3.33x33 TM3 hydrophobic
donitriptan C133 3.36x36 TM3 hydrophobic
donitriptan T134 3.37x37 TM3 polar (hydrogen bond)
donitriptan V201 45.52x52 ECL2 Van der Waals
donitriptan T203 ECL2 Van der Waals
donitriptan T209 5.39x40 TM5 Van der Waals
donitriptan S212 5.42x43 TM5 Van der Waals
donitriptan A216 5.46x461 TM5 Van der Waals
donitriptan W327 6.48x48 TM6 Van der Waals
donitriptan F330 6.51x51 TM6 hydrophobic
donitriptan F330 6.51x51 TM6 aromatic (pi-cation)
donitriptan F331 6.52x52 TM6 hydrophobic
donitriptan F331 6.52x52 TM6 aromatic (edge-to-face)
donitriptan I333 6.54x54 TM6 hydrophobic
donitriptan S334 6.55x55 TM6 Van der Waals
donitriptan M337 6.58x58 TM6 hydrophobic
donitriptan L348 7.32x31 TM7 Van der Waals
donitriptan F351 7.35x34 TM7 hydrophobic
donitriptan Y359 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
TM3
3x32 3.32x32 D129
3x33 3.33x33 I130
3x36 3.36x36 C133
3x37 3.37x37 T134
ECL2
45x52 45.52x52 V201
TM5
5x40 5.39x40 T209
5x43 5.42x43 S212
5x461 5.46x461 A216
TM6
6x48 6.48x48 W327
6x51 6.51x51 F330
6x52 6.52x52 F331
6x54 6.54x54 I333
6x55 6.55x55 S334
6x58 6.58x58 M337
TM7
7x31 7.32x31 L348
7x34 7.35x34 F351
7x42 7.43x42 Y359