Structure information

5-HT1A receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

8FYL

SPECIES

Homo sapiens

RESOLUTION

2.940

PREFERRED CHAIN

R

REFERENCE

10.1038/S41586-024-07403-2

PUBLICATION DATE

May 15, 2024

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
vilazodone A93 2.61x60 TM2 hydrophobic
vilazodone Y96 2.64x63 TM2 polar (hydrogen bond with backbone)
vilazodone Y96 2.64x63 TM2 aromatic (face-to-face)
vilazodone Y96 2.64x63 TM2 Van der Waals
vilazodone Q97 2.65x64 TM2 polar (hydrogen bond)
vilazodone N100 2.68x67 TM2 Van der Waals
vilazodone D116 3.32x32 TM3 polar (charge-assisted hydrogen bond)
vilazodone V117 3.33x33 TM3 hydrophobic
vilazodone V117 3.33x33 TM3 Van der Waals
vilazodone C120 3.36x36 TM3 Van der Waals
vilazodone C120 3.36x36 TM3 hydrophobic
vilazodone T121 3.37x37 TM3 polar (hydrogen bond)
vilazodone I189 45.52x52 ECL2 hydrophobic
vilazodone I189 45.52x52 ECL2 Van der Waals
vilazodone S199 5.42x43 TM5 Van der Waals
vilazodone A203 5.46x461 TM5 Van der Waals
vilazodone W358 6.48x48 TM6 hydrophobic
vilazodone W358 6.48x48 TM6 Van der Waals
vilazodone F361 6.51x51 TM6 hydrophobic
vilazodone F361 6.51x51 TM6 Van der Waals
vilazodone F362 6.52x52 TM6 aromatic (edge-to-face)
vilazodone F362 6.52x52 TM6 Van der Waals
vilazodone A365 6.55x55 TM6 Van der Waals
vilazodone N386 7.39x38 TM7 Van der Waals
vilazodone W387 7.40x39 TM7 Van der Waals
vilazodone W387 7.40x39 TM7 hydrophobic
vilazodone Y390 7.43x42 TM7 polar (hydrogen bond)

Ligands

vilazodone

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Residue Diagrams

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
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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
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Residue Table


GPCRdb(A)
GPCRdb(A)
5-HT1A receptor
TM2
2x60 2.61x60 A93
2x63 2.64x63 Y96
2x64 2.65x64 Q97
2x67 2.68x67 N100
TM3
3x32 3.32x32 D116
3x33 3.33x33 V117
3x36 3.36x36 C120
3x37 3.37x37 T121
ECL2
45x52 45.52x52 I189
TM5
5x43 5.42x43 S199
5x461 5.46x461 A203
TM6
6x48 6.48x48 W358
6x51 6.51x51 F361
6x52 6.52x52 F362
6x55 6.55x55 A365
TM7
7x38 7.39x38 N386
7x39 7.40x39 W387
7x42 7.43x42 Y390