PDB
9KVI
Resolution
2.5 Å
Released
Dec. 3, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligands
Function
bufotenine
Agonist
PtdIns4P
PAM
Reference
—
bufotenine PtdIns4P

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Ligand Amino Acid Generic Number Segment Interaction Type
bufotenine D116 3.32x32 TM3 polar (charge-charge)
bufotenine D116 3.32x32 TM3 polar (hydrogen bond)
bufotenine V117 3.33x33 TM3 Van der Waals
bufotenine C120 3.36x36 TM3 hydrophobic
bufotenine T121 3.37x37 TM3 polar (hydrogen bond)
PtdIns4P R134 3.50x50 TM3 polar (charge-charge)
bufotenine I167 4.56x56 TM4 Van der Waals
bufotenine I189 45.52x52 ECL2 Van der Waals
bufotenine S199 5.42x43 TM5 Van der Waals
bufotenine T200 5.43x44 TM5 Van der Waals
bufotenine A203 5.46x461 TM5 hydrophobic
PtdIns4P T346 6.36x36 TM6 Van der Waals
bufotenine W358 6.48x48 TM6 hydrophobic
bufotenine F361 6.51x51 TM6 hydrophobic
bufotenine F362 6.52x52 TM6 hydrophobic
bufotenine F362 6.52x52 TM6 aromatic (edge-to-face)
bufotenine A365 6.55x55 TM6 Van der Waals
bufotenine N386 7.39x38 TM7 Van der Waals
bufotenine Y390 7.43x42 TM7 Van der Waals
PtdIns4P I399 7.52x52 TM7 Van der Waals
PtdIns4P Y402 7.55x55 TM7 Van der Waals
PtdIns4P F403 7.56x56 TM7 hydrophobic
PtdIns4P K405 8.48x48 H8 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
5-HT1A receptor
TM3
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
3x37 3.37x37 T121
3x50 3.50x50 R134
TM4
4x56 4.56x56 I167
ECL2
45x52 45.52x52 I189
TM5
5x43 5.42x43 S199
5x44 5.43x44 T200
5x461 5.46x461 A203
TM6
6x36 6.36x36 T346
6x48 6.48x48 W358
6x51 6.51x51 F361
6x52 6.52x52 F362
6x55 6.55x55 A365
TM7
7x38 7.39x38 N386
7x42 7.43x42 Y390
7x52 7.52x52 I399
7x55 7.55x55 Y402
7x56 7.56x56 F403
H8
8x48 8.48x48 K405