PDB
7T6B
Resolution
3.2 Å
Released
April 6, 2022
Receptor
S1P2
Class
A
Species
Homo sapiens
Ligand
Function
sphingosine 1-phosphate
Agonist
Reference
10.1126/SCIADV.ABN0067

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Ligand Amino Acid Generic Number Segment Interaction Type
sphingosine 1-phosphate R33 1.32x32 TM1 polar (charge-charge)
sphingosine 1-phosphate N89 2.60x60 TM2 polar (hydrogen bond)
sphingosine 1-phosphate S93 2.64x64 TM2 Van der Waals
sphingosine 1-phosphate L98 23.51x501 ECL1 Van der Waals
sphingosine 1-phosphate R108 3.28x28 TM3 polar (charge-charge)
sphingosine 1-phosphate E109 3.29x29 TM3 hydrophobic
sphingosine 1-phosphate E109 3.29x29 TM3 polar (hydrogen bond)
sphingosine 1-phosphate E109 3.29x29 TM3 polar (charge-charge)
sphingosine 1-phosphate A112 3.32x32 TM3 hydrophobic
sphingosine 1-phosphate F113 3.33x33 TM3 hydrophobic
sphingosine 1-phosphate L116 3.36x36 TM3 Van der Waals
sphingosine 1-phosphate S117 3.37x37 TM3 Van der Waals
sphingosine 1-phosphate V120 3.40x40 TM3 Van der Waals
sphingosine 1-phosphate F121 3.41x41 TM3 hydrophobic
sphingosine 1-phosphate L162 4.56x56 TM4 Van der Waals
sphingosine 1-phosphate L183 ECL2 hydrophobic
sphingosine 1-phosphate V194 5.43x43 TM5 hydrophobic
sphingosine 1-phosphate I197 5.46x46 TM5 Van der Waals
sphingosine 1-phosphate F198 5.47x47 TM5 hydrophobic
sphingosine 1-phosphate W246 6.48x48 TM6 hydrophobic
sphingosine 1-phosphate H271 7.36x35 TM7 Van der Waals
sphingosine 1-phosphate F274 7.39x38 TM7 hydrophobic

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

GPCRdb(A)
GPCRdb(A)
S1P2 receptor
TM1
1x32 1.32x32 R33
TM2
2x60 2.60x60 N89
2x64 2.64x64 S93
ECL1
23x501 23.51x501 L98
TM3
3x28 3.28x28 R108
3x29 3.29x29 E109
3x32 3.32x32 A112
3x33 3.33x33 F113
3x36 3.36x36 L116
3x37 3.37x37 S117
3x40 3.40x40 V120
3x41 3.41x41 F121
TM4
4x56 4.56x56 L162
TM5
5x43 5.43x43 V194
5x46 5.46x46 I197
5x47 5.47x47 F198
TM6
6x48 6.48x48 W246
TM7
7x35 7.36x35 H271
7x38 7.39x38 F274