PDB
9W0H
Resolution
3.0 Å
Released
June 3, 2026
Receptor
S1P3
Class
A
Species
Homo sapiens
Ligands
SPM-242
Cpd-32
Function
Antagonist
Allosteric antagonist
Reference
—
SPM-242 Cpd-32

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Ligand Amino Acid Generic Number Segment Interaction Type
SPM-242 Y22 N-term Van der Waals
SPM-242 Y22 N-term polar (hydrogen bond)
SPM-242 T42 1.35x35 TM1 Van der Waals
Cpd-32 S84 2.49x49 TM2 polar (hydrogen bond with backbone)
Cpd-32 S84 2.49x49 TM2 Van der Waals
Cpd-32 L87 2.52x52 TM2 Van der Waals
Cpd-32 L87 2.52x52 TM2 hydrophobic
Cpd-32 A88 2.53x53 TM2 Van der Waals
Cpd-32 A91 2.56x56 TM2 Van der Waals
Cpd-32 V94 2.59x59 TM2 Van der Waals
SPM-242 N95 2.60x60 TM2 polar (hydrogen bond)
SPM-242 I96 2.61x61 TM2 hydrophobic
SPM-242 I96 2.61x61 TM2 Van der Waals
SPM-242 S99 2.64x64 TM2 polar (hydrogen bond)
SPM-242 S99 2.64x64 TM2 polar (hydrogen bond)
SPM-242 G100 23.47x47 ECL1 Van der Waals
SPM-242 G100 23.47x47 ECL1 polar (hydrogen bond with backbone)
SPM-242 T103 23.50x50 ECL1 Van der Waals
SPM-242 T103 23.50x50 ECL1 polar (hydrogen bond)
Cpd-32 L113 3.27x27 TM3 Van der Waals
Cpd-32 L113 3.27x27 TM3 polar (hydrogen bond with backbone)
SPM-242 R114 3.28x28 TM3 polar (charge-assisted hydrogen bond)
SPM-242 E115 3.29x29 TM3 polar (charge-assisted hydrogen bond)
Cpd-32 G116 3.30x30 TM3 Van der Waals
Cpd-32 S117 3.31x31 TM3 polar (hydrogen bond)
Cpd-32 V120 3.34x34 TM3 hydrophobic
Cpd-32 V120 3.34x34 TM3 Van der Waals
Cpd-32 A121 3.35x35 TM3 Van der Waals
Cpd-32 W162 4.50x50 TM4 Van der Waals
Cpd-32 F166 4.54x54 TM4 hydrophobic
Cpd-32 F166 4.54x54 TM4 Van der Waals
Cpd-32 G169 4.57x57 TM4 Van der Waals
SPM-242 Q460 7.36x35 TM7 Van der Waals
SPM-242 W461 7.37x36 TM7 Van der Waals
SPM-242 I463 7.39x38 TM7 hydrophobic
SPM-242 I463 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
TM1
1x35 1.35x35 T42
TM2
2x49 2.49x49 C84
2x52 2.52x52 L87
2x53 2.53x53 A88
2x56 2.56x56 A91
2x59 2.59x59 V94
2x60 2.60x60 N95
2x61 2.61x61 I96
2x64 2.64x64 S99
ECL1
23x47 23.47x47 G100
23x50 23.50x50 T103
TM3
3x27 3.27x27 L113
3x28 3.28x28 R114
3x29 3.29x29 E115
3x30 3.30x30 G116
3x31 3.31x31 S117
3x34 3.34x34 V120
3x35 3.35x35 A121
TM4
4x50 4.50x50 W162
4x54 4.54x54 F166
4x57 4.57x57 G169
TM7
7x35 7.36x35 Q281
7x36 7.37x36 W282
7x38 7.39x38 I284