PDB
4IAQ
Resolution
2.8 Å
Released
March 13, 2013
Receptor
5-HT1B
Class
A
Species
Homo sapiens
Ligand
Function
dihydroergotamine
Agonist
Reference
10.1126/SCIENCE.1232807

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Ligand Amino Acid Generic Number Segment Interaction Type
dihydroergotamine Y109 2.64x63 TM2 Van der Waals
dihydroergotamine W125 3.28x28 TM3 hydrophobic
dihydroergotamine L126 3.29x29 TM3 hydrophobic
dihydroergotamine D129 3.32x32 TM3 polar (hydrogen bond)
dihydroergotamine D129 3.32x32 TM3 polar (charge-charge)
dihydroergotamine I130 3.33x33 TM3 hydrophobic
dihydroergotamine C133 3.36x36 TM3 hydrophobic
dihydroergotamine T134 3.37x37 TM3 Van der Waals
dihydroergotamine C199 45.50x50 ECL2 Van der Waals
dihydroergotamine V200 45.51x51 ECL2 Van der Waals
dihydroergotamine V201 45.52x52 ECL2 polar (hydrogen bond with backbone)
dihydroergotamine V201 45.52x52 ECL2 hydrophobic
dihydroergotamine S212 5.42x43 TM5 Van der Waals
dihydroergotamine A216 5.46x461 TM5 Van der Waals
dihydroergotamine W327 6.48x48 TM6 Van der Waals
dihydroergotamine F330 6.51x51 TM6 hydrophobic
dihydroergotamine F331 6.52x52 TM6 hydrophobic
dihydroergotamine F331 6.52x52 TM6 aromatic (edge-to-face)
dihydroergotamine S334 6.55x55 TM6 Van der Waals
dihydroergotamine M337 6.58x58 TM6 hydrophobic
dihydroergotamine L348 7.32x31 TM7 hydrophobic
dihydroergotamine F351 7.35x34 TM7 hydrophobic
dihydroergotamine D352 7.36x35 TM7 Van der Waals
dihydroergotamine T355 7.39x38 TM7 Van der Waals
dihydroergotamine Y359 7.43x42 TM7 Van der Waals

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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
6x58 6.58x58 M337
TM7
7x31 7.32x31 L348
7x34 7.35x34 F351
7x35 7.36x35 D352
7x38 7.39x38 T355
7x42 7.43x42 Y359