PDB
9VMY
Resolution
2.9 Å
Released
Nov. 12, 2025
Receptor
5-HT1A
Class
A
Species
Homo sapiens
Ligand
Function
TMU4142
Agonist
Reference
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Ligand Amino Acid Generic Number Segment Interaction Type
TMU4142 Y96 2.64x63 TM2 Van der Waals
TMU4142 I113 3.29x29 TM3 Van der Waals
TMU4142 D116 3.32x32 TM3 polar (charge-charge)
TMU4142 D116 3.32x32 TM3 polar (hydrogen bond)
TMU4142 V117 3.33x33 TM3 hydrophobic
TMU4142 C120 3.36x36 TM3 Van der Waals
TMU4142 T121 3.37x37 TM3 Van der Waals
TMU4142 I167 4.56x56 TM4 Van der Waals
TMU4142 C187 45.50x50 ECL2 Van der Waals
TMU4142 T188 45.51x51 ECL2 Van der Waals
TMU4142 I189 45.52x52 ECL2 hydrophobic
TMU4142 I189 45.52x52 ECL2 polar (hydrogen bond with backbone)
TMU4142 S199 5.42x43 TM5 polar (hydrogen bond)
TMU4142 T200 5.43x44 TM5 Van der Waals
TMU4142 A203 5.46x461 TM5 hydrophobic
TMU4142 W358 6.48x48 TM6 Van der Waals
TMU4142 F361 6.51x51 TM6 hydrophobic
TMU4142 F362 6.52x52 TM6 aromatic (edge-to-face)
TMU4142 F362 6.52x52 TM6 hydrophobic
TMU4142 V364 6.54x54 TM6 hydrophobic
TMU4142 A365 6.55x55 TM6 Van der Waals
TMU4142 L368 6.58x58 TM6 hydrophobic
TMU4142 M377 ECL3 hydrophobic
TMU4142 G382 7.35x34 TM7 Van der Waals
TMU4142 I385 7.38x37 TM7 Van der Waals
TMU4142 N386 7.39x38 TM7 polar (hydrogen bond)
TMU4142 N386 7.39x38 TM7 hydrophobic
TMU4142 N386 7.39x38 TM7 polar (hydrogen bond)
TMU4142 Y390 7.43x42 TM7 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
2x63 2.64x63 Y96
TM3
3x29 3.29x29 I113
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
3x37 3.37x37 T121
TM4
4x56 4.56x56 I167
ECL2
45x50 45.50x50 C187
45x51 45.51x51 T188
45x52 45.52x52 I189
TM5
5x43 5.42x43 S199
5x44 5.43x44 T200
5x461 5.46x461 A203
TM6
6x48 6.48x48 W358
6x51 6.51x51 F361
6x52 6.52x52 F362
6x54 6.54x54 V364
6x55 6.55x55 A365
6x58 6.58x58 L368
TM7
7x34 7.35x34 G382
7x37 7.38x37 I385
7x38 7.39x38 N386
7x42 7.43x42 Y390