PDB
9VNZ
Resolution
2.8 Å
Released
Jan. 28, 2026
Receptor
S1P1
Class
A
Species
Homo sapiens
Ligand
HY-X-1011
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
HY-X-1011 Y29 N-term polar (hydrogen bond)
HY-X-1011 Y29 N-term Van der Waals
HY-X-1011 N101 2.60x60 TM2 polar (hydrogen bond)
HY-X-1011 N101 2.60x60 TM2 Van der Waals
HY-X-1011 S105 2.64x64 TM2 Van der Waals
HY-X-1011 G106 23.47x47 ECL1 Van der Waals
HY-X-1011 T109 23.50x50 ECL1 Van der Waals
HY-X-1011 R120 3.28x28 TM3 Van der Waals
HY-X-1011 E121 3.29x29 TM3 polar (charge-assisted hydrogen bond)
HY-X-1011 F125 3.33x33 TM3 aromatic (face-to-face)
HY-X-1011 F125 3.33x33 TM3 Van der Waals
HY-X-1011 L128 3.36x36 TM3 hydrophobic
HY-X-1011 L128 3.36x36 TM3 Van der Waals
HY-X-1011 S129 3.37x37 TM3 Van der Waals
HY-X-1011 V132 3.40x40 TM3 Van der Waals
HY-X-1011 V132 3.40x40 TM3 hydrophobic
HY-X-1011 C206 5.43x43 TM5 Van der Waals
HY-X-1011 C206 5.43x43 TM5 polar (hydrogen bond with backbone)
HY-X-1011 T207 5.44x44 TM5 Van der Waals
HY-X-1011 V209 5.46x46 TM5 Van der Waals
HY-X-1011 F210 5.47x47 TM5 Van der Waals
HY-X-1011 F210 5.47x47 TM5 hydrophobic
HY-X-1011 W269 6.48x48 TM6 hydrophobic
HY-X-1011 W269 6.48x48 TM6 Van der Waals
HY-X-1011 L272 6.51x51 TM6 Van der Waals
HY-X-1011 L276 6.55x55 TM6 hydrophobic
HY-X-1011 L276 6.55x55 TM6 Van der Waals
HY-X-1011 L297 7.39x38 TM7 hydrophobic
HY-X-1011 L297 7.39x38 TM7 Van der Waals

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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
2x64 2.64x64 S105
ECL1
23x47 23.47x47 G106
23x50 23.50x50 T109
TM3
3x28 3.28x28 R120
3x29 3.29x29 E121
3x33 3.33x33 F125
3x36 3.36x36 L128
3x37 3.37x37 S129
3x40 3.40x40 V132
TM5
5x43 5.43x43 C206
5x44 5.44x44 T207
5x46 5.46x46 V209
5x47 5.47x47 F210
TM6
6x48 6.48x48 W269
6x51 6.51x51 L272
6x55 6.55x55 L276
TM7
7x38 7.39x38 L297