PDB
9KVG
Resolution
2.6 Å
Released
Dec. 3, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligands
PtdIns4P
5-MeO-DMT
Function
PAM
Agonist
Reference
10.34133/RESEARCH.0987
PtdIns4P 5-MeO-DMT

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Ligand Amino Acid Generic Number Segment Interaction Type
PtdIns4P L52 1.48x48 TM1 hydrophobic
PtdIns4P L52 1.48x48 TM1 Van der Waals
PtdIns4P G53 1.49x49 TM1 Van der Waals
5-MeO-DMT D116 3.32x32 TM3 polar (charge-assisted hydrogen bond)
5-MeO-DMT V117 3.33x33 TM3 hydrophobic
5-MeO-DMT V117 3.33x33 TM3 Van der Waals
5-MeO-DMT C120 3.36x36 TM3 Van der Waals
5-MeO-DMT T121 3.37x37 TM3 Van der Waals
PtdIns4P R134 3.50x50 TM3 polar (charge-assisted hydrogen bond)
5-MeO-DMT I189 45.52x52 ECL2 hydrophobic
5-MeO-DMT I189 45.52x52 ECL2 Van der Waals
5-MeO-DMT T196 5.39x40 TM5 Van der Waals
5-MeO-DMT S199 5.42x43 TM5 Van der Waals
5-MeO-DMT T200 5.43x44 TM5 Van der Waals
5-MeO-DMT A203 5.46x461 TM5 Van der Waals
PtdIns4P K345 6.35x35 TM6 polar (charge-assisted hydrogen bond)
PtdIns4P T346 6.36x36 TM6 Van der Waals
PtdIns4P I349 6.39x39 TM6 hydrophobic
5-MeO-DMT W358 6.48x48 TM6 Van der Waals
5-MeO-DMT F361 6.51x51 TM6 aromatic (edge-to-face)
5-MeO-DMT F361 6.51x51 TM6 Van der Waals
5-MeO-DMT F362 6.52x52 TM6 hydrophobic
5-MeO-DMT F362 6.52x52 TM6 Van der Waals
5-MeO-DMT N386 7.39x38 TM7 Van der Waals
5-MeO-DMT Y390 7.43x42 TM7 Van der Waals
5-MeO-DMT Y390 7.43x42 TM7 hydrophobic
PtdIns4P V398 7.51x51 TM7 hydrophobic
PtdIns4P V398 7.51x51 TM7 Van der Waals
PtdIns4P I399 7.52x52 TM7 Van der Waals
PtdIns4P I399 7.52x52 TM7 polar (hydrogen bond with backbone)
PtdIns4P Y402 7.55x55 TM7 hydrophobic
PtdIns4P Y402 7.55x55 TM7 Van der Waals
PtdIns4P F403 7.56x56 TM7 polar (hydrogen bond with backbone)
PtdIns4P F403 7.56x56 TM7 Van der Waals
PtdIns4P N404 8.47x47 H8 Van der Waals
PtdIns4P K405 8.48x48 H8 polar (charge-assisted 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
TM1
1x48 1.48x48 L52
1x49 1.49x49 G53
TM3
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
3x37 3.37x37 T121
3x50 3.50x50 R134
ECL2
45x52 45.52x52 I189
TM5
5x40 5.39x40 T196
5x43 5.42x43 S199
5x44 5.43x44 T200
5x461 5.46x461 A203
TM6
6x35 6.35x35 K345
6x36 6.36x36 T346
6x39 6.39x39 I349
6x48 6.48x48 W358
6x51 6.51x51 F361
6x52 6.52x52 F362
TM7
7x38 7.39x38 N386
7x42 7.43x42 Y390
7x51 7.51x51 V398
7x52 7.52x52 I399
7x55 7.55x55 Y402
7x56 7.56x56 F403
H8
8x47 8.47x47 N404
8x48 8.48x48 K405