PDB
7TD3
Resolution
3.0 Å
Released
Feb. 9, 2022
Receptor
S1P1
Class
A
Species
Homo sapiens
Ligand
Function
sphingosine 1-phosphate
Agonist
Reference
10.1038/S41467-022-28417-2

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Ligand Amino Acid Generic Number Segment Interaction Type
sphingosine 1-phosphate Y29 N-term polar (hydrogen bond)
sphingosine 1-phosphate K34 N-term polar (hydrogen bond)
sphingosine 1-phosphate K34 N-term polar (charge-charge)
sphingosine 1-phosphate N101 2.60x60 TM2 polar (hydrogen bond)
sphingosine 1-phosphate S105 ECL1 Van der Waals
sphingosine 1-phosphate G106 23.47x47 ECL1 polar (hydrogen bond with backbone)
sphingosine 1-phosphate T109 23.50x50 ECL1 polar (hydrogen bond)
sphingosine 1-phosphate R120 3.28x28 TM3 polar (hydrogen bond)
sphingosine 1-phosphate R120 3.28x28 TM3 polar (charge-charge)
sphingosine 1-phosphate E121 3.29x29 TM3 polar (charge-charge)
sphingosine 1-phosphate M124 3.32x32 TM3 hydrophobic
sphingosine 1-phosphate F125 3.33x33 TM3 hydrophobic
sphingosine 1-phosphate L128 3.36x36 TM3 hydrophobic
sphingosine 1-phosphate S129 3.37x37 TM3 Van der Waals
sphingosine 1-phosphate V132 3.40x40 TM3 Van der Waals
sphingosine 1-phosphate F133 3.41x41 TM3 hydrophobic
sphingosine 1-phosphate L174 4.56x56 TM4 Van der Waals
sphingosine 1-phosphate L195 ECL2 hydrophobic
sphingosine 1-phosphate C206 5.43x43 TM5 Van der Waals
sphingosine 1-phosphate V209 5.46x46 TM5 hydrophobic
sphingosine 1-phosphate F210 5.47x47 TM5 Van der Waals
sphingosine 1-phosphate L213 5.50x50 TM5 hydrophobic
sphingosine 1-phosphate W269 6.48x48 TM6 Van der Waals
sphingosine 1-phosphate L272 6.51x51 TM6 hydrophobic
sphingosine 1-phosphate L276 6.55x55 TM6 Van der Waals
sphingosine 1-phosphate L297 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
S1P1 receptor
TM2
2x60 2.60x60 N101
ECL1
23x47 23.47x47 G106
23x50 23.50x50 T109
TM3
3x28 3.28x28 R120
3x29 3.29x29 E121
3x32 3.32x32 M124
3x33 3.33x33 F125
3x36 3.36x36 L128
3x37 3.37x37 S129
3x40 3.40x40 V132
3x41 3.41x41 F133
TM4
4x56 4.56x56 L174
TM5
5x43 5.43x43 C206
5x46 5.46x46 V209
5x47 5.47x47 F210
5x50 5.50x50 L213
TM6
6x48 6.48x48 W269
6x51 6.51x51 L272
6x55 6.55x55 L276
TM7
7x38 7.39x38 L297