PDB
9GL2
Resolution
3.2 Å
Released
July 2, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligands
Befiradol
Phosphatidylinositol-4-phosphate
Function
Agonist
PAM
Reference
10.1126/SCIADV.ADV9267
Befiradol Phosphatidylinositol-4-phosphate

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Ligand Amino Acid Generic Number Segment Interaction Type
Befiradol A93 2.61x60 TM2 hydrophobic
Befiradol Y96 2.64x63 TM2 hydrophobic
Befiradol F112 3.28x28 TM3 hydrophobic
Befiradol I113 3.29x29 TM3 hydrophobic
Befiradol V117 3.33x33 TM3 hydrophobic
Befiradol C187 45.50x50 ECL2 hydrophobic
Befiradol I189 45.52x52 ECL2 hydrophobic
Befiradol A203 5.46x461 TM5 hydrophobic
Phosphatidylinositol-4-phosphate K345 6.35x35 TM6 polar (charge-assisted hydrogen bond)
Phosphatidylinositol-4-phosphate T346 6.36x36 TM6 Van der Waals
Phosphatidylinositol-4-phosphate T346 6.36x36 TM6 polar (hydrogen bond)
Befiradol F361 6.51x51 TM6 hydrophobic
Befiradol F362 6.52x52 TM6 aromatic (edge-to-face)
Befiradol N386 7.39x38 TM7 Van der Waals
Befiradol N386 7.39x38 TM7 polar (hydrogen bond)
Befiradol Y390 7.43x42 TM7 Van der Waals
Befiradol Y390 7.43x42 TM7 hydrophobic
Phosphatidylinositol-4-phosphate I399 7.52x52 TM7 polar (hydrogen bond with backbone)
Phosphatidylinositol-4-phosphate I399 7.52x52 TM7 Van der Waals
Phosphatidylinositol-4-phosphate Y400 7.53x53 TM7 Van der Waals
Phosphatidylinositol-4-phosphate F403 7.56x56 TM7 polar (hydrogen bond with backbone)
Phosphatidylinositol-4-phosphate F403 7.56x56 TM7 Van der Waals
Phosphatidylinositol-4-phosphate N404 8.47x47 H8 Van der Waals
Phosphatidylinositol-4-phosphate K405 8.48x48 H8 Van der Waals

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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
TM3
3x28 3.28x28 F112
3x29 3.29x29 I113
3x33 3.33x33 V117
ECL2
45x50 45.50x50 C187
45x52 45.52x52 I189
TM5
5x461 5.46x461 A203
TM6
6x35 6.35x35 K345
6x36 6.36x36 T346
6x51 6.51x51 F361
6x52 6.52x52 F362
TM7
7x38 7.39x38 N386
7x42 7.43x42 Y390
7x52 7.52x52 I399
7x53 7.53x53 Y400
7x56 7.56x56 F403
H8
8x47 8.47x47 N404
8x48 8.48x48 K405