Structure information

S1P5 receptor

PROTEIN CLASS

Class A (Rhodopsin)

PDB CODE

7YXA

SPECIES

Homo sapiens

RESOLUTION

2.200

PREFERRED CHAIN

A

REFERENCE

10.1038/S41467-022-32447-1

PUBLICATION DATE

Aug. 10, 2022

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Ligand Interaction Browser

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Ligand Amino Acid Generic Number Segment Interaction Type
Ligand Amino Acid Generic Number Segment Interaction Type
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid Y19 N-term polar (hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid K24 N-term polar (charge-assisted hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid C43 1.39x39 TM1 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid Y89 2.57x57 TM2 polar (hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid N92 2.60x60 TM2 polar (hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid I93 2.61x61 TM2 hydrophobic
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid I93 2.61x61 TM2 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid W108 3.25x25 TM3 polar (hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid R111 3.28x28 TM3 polar (charge-assisted hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid E112 3.29x29 TM3 polar (charge-charge)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid E112 3.29x29 TM3 polar (charge-assisted hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid V115 3.32x32 TM3 hydrophobic
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid V115 3.32x32 TM3 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid V185 ECL2 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid V185 ECL2 polar (hydrogen bond with backbone)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid L186 ECL2 hydrophobic
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid L186 ECL2 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid P187 ECL2 polar (hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid W264 6.48x48 TM6 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid L267 6.51x51 TM6 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid D289 7.36x35 TM7 polar (hydrogen bond with backbone)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid D289 7.36x35 TM7 polar (charge-assisted hydrogen bond)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid L292 7.39x38 TM7 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid L292 7.39x38 TM7 polar (hydrogen bond with backbone)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid G293 7.40x39 TM7 polar (hydrogen bond with backbone)
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid G293 7.40x39 TM7 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid A295 7.42x41 TM7 Van der Waals
4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid M296 7.43x42 TM7 polar (hydrogen bond)

Ligands

4-[6-(2-naphthalen-1-ylethoxy)-2,3,4,5-tetrahydro-1H-3-benzazepin-3-ium-3-yl]butanoic acid

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Residue Diagrams

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
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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
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Residue Table


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