PDB
7YXA
Resolution
2.2 Å
Released
Aug. 10, 2022
Receptor
S1P5
Class
A
Species
Homo sapiens
Ligand
CHEMBL6059624
Function
Inverse agonist
Reference
10.1038/S41467-022-32447-1

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Ligand Amino Acid Generic Number Segment Interaction Type
CHEMBL6059624 Y19 N-term polar (hydrogen bond)
CHEMBL6059624 Y19 N-term polar (hydrogen bond)
CHEMBL6059624 K24 N-term polar (charge-assisted hydrogen bond)
CHEMBL6059624 C43 1.39x39 TM1 Van der Waals
CHEMBL6059624 Y89 2.57x57 TM2 polar (hydrogen bond)
CHEMBL6059624 N92 2.60x60 TM2 polar (hydrogen bond)
CHEMBL6059624 I93 2.61x61 TM2 Van der Waals
CHEMBL6059624 W108 3.25x25 TM3 Van der Waals
CHEMBL6059624 R111 3.28x28 TM3 polar (charge-assisted hydrogen bond)
CHEMBL6059624 E112 3.29x29 TM3 polar (charge-assisted hydrogen bond)
CHEMBL6059624 E112 3.29x29 TM3 polar (charge-charge)
CHEMBL6059624 V115 3.32x32 TM3 Van der Waals
CHEMBL6059624 V115 3.32x32 TM3 hydrophobic
CHEMBL6059624 V185 ECL2 polar (hydrogen bond with backbone)
CHEMBL6059624 V185 ECL2 Van der Waals
CHEMBL6059624 L186 ECL2 Van der Waals
CHEMBL6059624 P187 ECL2 Van der Waals
CHEMBL6059624 W264 6.48x48 TM6 hydrophobic
CHEMBL6059624 W264 6.48x48 TM6 Van der Waals
CHEMBL6059624 L267 6.51x51 TM6 Van der Waals
CHEMBL6059624 D289 7.36x35 TM7 polar (hydrogen bond with backbone)
CHEMBL6059624 D289 7.36x35 TM7 polar (charge-assisted hydrogen bond)
CHEMBL6059624 L292 7.39x38 TM7 polar (hydrogen bond with backbone)
CHEMBL6059624 L292 7.39x38 TM7 Van der Waals
CHEMBL6059624 G293 7.40x39 TM7 polar (hydrogen bond with backbone)
CHEMBL6059624 G293 7.40x39 TM7 Van der Waals
CHEMBL6059624 A295 7.42x41 TM7 Van der Waals
CHEMBL6059624 M296 7.43x42 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
S1P5 receptor
TM1
1x39 1.39x39 C43
TM2
2x57 2.57x57 Y89
2x60 2.60x60 N92
2x61 2.61x61 I93
TM3
3x25 3.25x25 W108
3x28 3.28x28 R111
3x29 3.29x29 E112
3x32 3.32x32 V115
TM6
6x48 6.48x48 W264
6x51 6.51x51 L267
TM7
7x35 7.36x35 D289
7x38 7.39x38 L292
7x39 7.40x39 G293
7x41 7.42x41 A295
7x42 7.43x42 M296