PDB
7EW4
Resolution
3.2 Å
Released
Sept. 29, 2021
Receptor
S1P3
Class
A
Species
Homo sapiens
Ligand
Function
CYM-5541
Agonist
Reference
10.1038/S41422-021-00567-W

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Ligand Amino Acid Generic Number Segment Interaction Type
CYM-5541 M118 3.32x32 TM3 hydrophobic
CYM-5541 F119 3.33x33 TM3 aromatic (edge-to-face)
CYM-5541 F119 3.33x33 TM3 hydrophobic
CYM-5541 L122 3.36x36 TM3 hydrophobic
CYM-5541 G123 3.37x37 TM3 Van der Waals
CYM-5541 T126 3.40x40 TM3 Van der Waals
CYM-5541 L168 4.56x56 TM4 hydrophobic
CYM-5541 L189 ECL2 Van der Waals
CYM-5541 C200 5.43x43 TM5 hydrophobic
CYM-5541 I201 5.44x44 TM5 hydrophobic
CYM-5541 I203 5.46x46 TM5 hydrophobic
CYM-5541 F204 5.47x47 TM5 hydrophobic
CYM-5541 I207 5.50x50 TM5 Van der Waals
CYM-5541 W256 6.48x48 TM6 hydrophobic
CYM-5541 L259 6.51x51 TM6 Van der Waals
CYM-5541 F260 6.52x52 TM6 Van der Waals
CYM-5541 F263 6.55x55 TM6 hydrophobic
CYM-5541 F263 6.55x55 TM6 aromatic (edge-to-face)
CYM-5541 I284 7.39x38 TM7 hydrophobic

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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
TM3
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
5x43 5.43x43 C200
5x44 5.44x44 I201
5x46 5.46x46 I203
5x47 5.47x47 F204
5x50 5.50x50 I207
TM6
6x48 6.48x48 W256
6x51 6.51x51 L259
6x52 6.52x52 F260
6x55 6.55x55 F263
TM7
7x38 7.39x38 I284