PDB
9VNF
Resolution
2.7 Å
Released
Nov. 12, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligand
(-)-pindolol
Function
Agonist (partial)
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
(-)-pindolol D116 3.32x32 TM3 polar (charge-assisted hydrogen bond)
(-)-pindolol V117 3.33x33 TM3 Van der Waals
(-)-pindolol V117 3.33x33 TM3 hydrophobic
(-)-pindolol C120 3.36x36 TM3 Van der Waals
(-)-pindolol I189 45.52x52 ECL2 hydrophobic
(-)-pindolol I189 45.52x52 ECL2 Van der Waals
(-)-pindolol S199 5.42x43 TM5 polar (hydrogen bond)
(-)-pindolol T200 5.43x44 TM5 Van der Waals
(-)-pindolol W358 6.48x48 TM6 hydrophobic
(-)-pindolol W358 6.48x48 TM6 Van der Waals
(-)-pindolol F361 6.51x51 TM6 Van der Waals
(-)-pindolol F361 6.51x51 TM6 aromatic (edge-to-face)
(-)-pindolol F362 6.52x52 TM6 aromatic (edge-to-face)
(-)-pindolol F362 6.52x52 TM6 Van der Waals
(-)-pindolol A365 6.55x55 TM6 Van der Waals
(-)-pindolol N386 7.39x38 TM7 polar (hydrogen bond)
(-)-pindolol N386 7.39x38 TM7 polar (hydrogen bond)
(-)-pindolol Y390 7.43x42 TM7 polar (hydrogen bond)
(-)-pindolol Y390 7.43x42 TM7 polar (hydrogen bond)

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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
ECL2
45x52 45.52x52 I189
TM5
5x43 5.42x43 S199
5x44 5.43x44 T200
TM6
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