PDB
9MD1
Resolution
3.0 Å
Released
Aug. 13, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligands
buspirone
PtdIns4P
Function
Agonist
PAM
Reference
10.1126/SCIADV.ADU9851
buspirone PtdIns4P

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Ligand Amino Acid Generic Number Segment Interaction Type
buspirone A93 2.61x60 TM2 hydrophobic
buspirone Y96 2.64x63 TM2 hydrophobic
buspirone W102 23.50x50 ECL1 hydrophobic
buspirone F112 3.28x28 TM3 hydrophobic
buspirone D116 3.32x32 TM3 polar (charge-assisted hydrogen bond)
buspirone V117 3.33x33 TM3 hydrophobic
buspirone V117 3.33x33 TM3 Van der Waals
buspirone C120 3.36x36 TM3 Van der Waals
buspirone C187 45.50x50 ECL2 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 Van der Waals
buspirone F361 6.51x51 TM6 hydrophobic
buspirone F361 6.51x51 TM6 Van der Waals
buspirone F362 6.52x52 TM6 aromatic (edge-to-face)
buspirone F362 6.52x52 TM6 Van der Waals
buspirone N386 7.39x38 TM7 Van der Waals
buspirone Y390 7.43x42 TM7 Van der Waals
buspirone Y390 7.43x42 TM7 hydrophobic
PtdIns4P V398 7.51x51 TM7 Van der Waals
PtdIns4P V398 7.51x51 TM7 hydrophobic
PtdIns4P I399 7.52x52 TM7 Van der Waals
PtdIns4P I399 7.52x52 TM7 polar (hydrogen bond with backbone)
PtdIns4P Y400 7.53x53 TM7 Van der Waals
PtdIns4P Y400 7.53x53 TM7 polar (hydrogen bond with backbone)
PtdIns4P Y402 7.55x55 TM7 Van der Waals
PtdIns4P Y402 7.55x55 TM7 hydrophobic
PtdIns4P F403 7.56x56 TM7 Van der Waals
PtdIns4P F403 7.56x56 TM7 polar (hydrogen bond with backbone)
PtdIns4P N404 8.47x47 H8 Van der Waals
PtdIns4P N404 8.47x47 H8 polar (hydrogen bond with backbone)

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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
TM2
2x60 2.61x60 A93
2x63 2.64x63 Y96
ECL1
23x50 23.50x50 W102
TM3
3x28 3.28x28 F112
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
ECL2
45x50 45.50x50 C187
TM6
6x35 6.35x35 K345
6x36 6.36x36 T346
6x39 6.39x39 I349
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
7x53 7.53x53 Y400
7x55 7.55x55 Y402
7x56 7.56x56 F403
H8
8x47 8.47x47 N404