PDB
9WP9
Resolution
3.3 Å
Released
Nov. 26, 2025
Receptor
S1P3
Class
A
Species
Homo sapiens
Ligand
sphingosine 1-phosphate
Function
Agonist
Reference
10.1073/PNAS.2507421122

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Ligand Amino Acid Generic Number Segment Interaction Type
sphingosine 1-phosphate Y22 N-term polar (hydrogen bond)
sphingosine 1-phosphate Y22 N-term Van der Waals
sphingosine 1-phosphate N95 2.60x60 TM2 polar (hydrogen bond)
sphingosine 1-phosphate S99 2.64x64 TM2 polar (hydrogen bond)
sphingosine 1-phosphate S99 2.64x64 TM2 polar (hydrogen bond)
sphingosine 1-phosphate T103 23.50x50 ECL1 Van der Waals
sphingosine 1-phosphate T103 23.50x50 ECL1 polar (hydrogen bond)
sphingosine 1-phosphate E115 3.29x29 TM3 Van der Waals
sphingosine 1-phosphate M118 3.32x32 TM3 hydrophobic
sphingosine 1-phosphate M118 3.32x32 TM3 Van der Waals
sphingosine 1-phosphate F119 3.33x33 TM3 Van der Waals
sphingosine 1-phosphate F119 3.33x33 TM3 hydrophobic
sphingosine 1-phosphate L122 3.36x36 TM3 hydrophobic
sphingosine 1-phosphate L122 3.36x36 TM3 Van der Waals
sphingosine 1-phosphate G123 3.37x37 TM3 Van der Waals
sphingosine 1-phosphate T126 3.40x40 TM3 Van der Waals
sphingosine 1-phosphate L168 4.56x56 TM4 Van der Waals
sphingosine 1-phosphate I188 ECL2 Van der Waals
sphingosine 1-phosphate L189 ECL2 hydrophobic
sphingosine 1-phosphate L189 ECL2 Van der Waals
sphingosine 1-phosphate I203 5.46x46 TM5 Van der Waals
sphingosine 1-phosphate W256 6.48x48 TM6 Van der Waals
sphingosine 1-phosphate W256 6.48x48 TM6 hydrophobic
sphingosine 1-phosphate L259 6.51x51 TM6 hydrophobic
sphingosine 1-phosphate L259 6.51x51 TM6 Van der Waals
sphingosine 1-phosphate F260 6.52x52 TM6 Van der Waals
sphingosine 1-phosphate F260 6.52x52 TM6 hydrophobic
sphingosine 1-phosphate F263 6.55x55 TM6 hydrophobic
sphingosine 1-phosphate F263 6.55x55 TM6 Van der Waals
sphingosine 1-phosphate I284 7.39x38 TM7 hydrophobic
sphingosine 1-phosphate I284 7.39x38 TM7 Van der Waals

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Snake plot — Download: PNG | SVG
ICL1 N K F H ICL1ECL1 G K K T F S L ECL1ICL2 M R P Y D A N ICL2ECL2 W N C L H N L P D C S T I L P L Y ECL2ICL3 V A ICL3ECL3 R V Q A C ECL3N-term M A T A L P P R L Q P V R G N E T L R E H Y Q Y V G K L A G R L K E A S E G N-termC-term N C L V R G R G A R A S P I Q P A L D P S R S K S S S S N N S S H S P K V K E D L P H T A P S S C I M D K N A A L Q N G I F C N C-term S T L T T V L F L V I C S F I V L E N L M V L I A I W K N N R M Y F F I G N L A L C D L L A G I A Y K V N I L M S S P T V W F L R E G S M F V A L G A S T C S L L A I A I E R H L T M I K K R H R V F L L I G M C W L I A F T L G A L P I L G S K K Y I A F C I S I F T A I L V T I V I L Y A R I Y F L V K S S S R K N H N N S E R S M A L L R T V V I V V S V F I A C W S P L F I L F L I D V A C P I L F K A Q W F I V L A V L N S A M N P V I Y T L A S K E F F R M R R A L V C
Helix box plot — Download: PNG | SVG L N E L V I F S C I V L F L V T T L T S 1 G N L A L C D L L A G I A Y K V N I L M 2 A L L S C T S A G L A V F M S G E R L F 3 V F L L I G M C W L I A F T L G A L P I 4 Y L I V I T V L I A T F I S I C F A I Y 5 V I V V S V F I A C W S P L F I L F L I 6 V P N M A S N L V A L V I F W Q A K F 7

GPCRdb(A)
GPCRdb(A)
S1P3 receptor
TM2
2x60 2.60x60 N95
2x64 2.64x64 S99
ECL1
23x50 23.50x50 T103
TM3
3x29 3.29x29 E115
3x32 3.32x32 M118
3x33 3.33x33 F119
3x36 3.36x36 L122
3x37 3.37x37 G123
3x40 3.40x40 T126
TM4
4x56 4.56x56 L168
TM5
5x46 5.46x46 I203
TM6
6x48 6.48x48 W256
6x51 6.51x51 L259
6x52 6.52x52 F260
6x55 6.55x55 F263
TM7
7x38 7.39x38 I284