PDB
7TD4
Resolution
2.6 Å
Released
Feb. 9, 2022
Receptor
S1P1
Class
A
Species
Homo sapiens
Ligand
Function
siponimod
Agonist
Reference
10.1038/S41467-022-28417-2

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Ligand Amino Acid Generic Number Segment Interaction Type
siponimod Y29 N-term Van der Waals
siponimod K34 N-term polar (charge-charge)
siponimod N101 2.60x60 TM2 Van der Waals
siponimod S105 ECL1 Van der Waals
siponimod T109 23.50x50 ECL1 polar (hydrogen bond)
siponimod R120 3.28x28 TM3 polar (charge-charge)
siponimod E121 3.29x29 TM3 polar (charge-charge)
siponimod E121 3.29x29 TM3 polar (hydrogen bond)
siponimod M124 3.32x32 TM3 Van der Waals
siponimod F125 3.33x33 TM3 hydrophobic
siponimod F125 3.33x33 TM3 aromatic (face-to-face)
siponimod L128 3.36x36 TM3 hydrophobic
siponimod S129 3.37x37 TM3 Van der Waals
siponimod V132 3.40x40 TM3 hydrophobic
siponimod F133 3.41x41 TM3 Van der Waals
siponimod L174 4.56x56 TM4 hydrophobic
siponimod V194 ECL2 hydrophobic
siponimod L195 ECL2 hydrophobic
siponimod C206 5.43x43 TM5 hydrophobic
siponimod T207 5.44x44 TM5 Van der Waals
siponimod V209 5.46x46 TM5 hydrophobic
siponimod F210 5.47x47 TM5 hydrophobic
siponimod L213 5.50x50 TM5 hydrophobic
siponimod W269 6.48x48 TM6 aromatic (edge-to-face)
siponimod L276 6.55x55 TM6 hydrophobic
siponimod A293 7.35x34 TM7 Van der Waals
siponimod E294 7.36x35 TM7 Van der Waals
siponimod 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
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
5x44 5.44x44 T207
5x46 5.46x46 V209
5x47 5.47x47 F210
5x50 5.50x50 L213
TM6
6x48 6.48x48 W269
6x55 6.55x55 L276
TM7
7x34 7.35x34 A293
7x35 7.36x35 E294
7x38 7.39x38 L297