PDB
8KGG
Resolution
3.1 Å
Released
July 31, 2024
Receptor
P2RY10
Class
A
Species
Homo sapiens
Ligand
LysoPS(18:0)
Function
Agonist
Reference
10.1016/J.CHEMBIOL.2024.08.005

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Ligand Amino Acid Generic Number Segment Interaction Type
LysoPS(18:0) Y37 1.35x35 TM1 polar (hydrogen bond)
LysoPS(18:0) Y37 1.35x35 TM1 Van der Waals
LysoPS(18:0) Y41 1.39x39 TM1 Van der Waals
LysoPS(18:0) R90 2.60x60 TM2 polar (charge-assisted hydrogen bond)
LysoPS(18:0) Y94 2.64x64 TM2 Van der Waals
LysoPS(18:0) F110 3.29x29 TM3 Van der Waals
LysoPS(18:0) Y114 3.33x33 TM3 polar (hydrogen bond)
LysoPS(18:0) Y114 3.33x33 TM3 Van der Waals
LysoPS(18:0) Y118 3.37x37 TM3 hydrophobic
LysoPS(18:0) Y118 3.37x37 TM3 Van der Waals
LysoPS(18:0) V160 4.53x53 TM4 hydrophobic
LysoPS(18:0) V160 4.53x53 TM4 Van der Waals
LysoPS(18:0) F167 4.60x60 TM4 hydrophobic
LysoPS(18:0) F167 4.60x60 TM4 Van der Waals
LysoPS(18:0) R171 ECL2 polar (charge-assisted hydrogen bond)
LysoPS(18:0) F182 45.51x51 ECL2 Van der Waals
LysoPS(18:0) A183 45.52x52 ECL2 polar (hydrogen bond with backbone)
LysoPS(18:0) A183 45.52x52 ECL2 Van der Waals
LysoPS(18:0) M198 5.38x39 TM5 Van der Waals
LysoPS(18:0) A202 5.42x43 TM5 hydrophobic
LysoPS(18:0) A202 5.42x43 TM5 Van der Waals
LysoPS(18:0) A205 5.45x46 TM5 Van der Waals
LysoPS(18:0) Y266 6.58x58 TM6 hydrophobic
LysoPS(18:0) Y266 6.58x58 TM6 Van der Waals
LysoPS(18:0) H287 7.35x34 TM7 Van der Waals
LysoPS(18:0) L291 7.39x38 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
P2RY10
TM1
1x35 1.35x35 Y37
1x39 1.39x39 Y41
TM2
2x60 2.60x60 R90
2x64 2.64x64 Y94
TM3
3x29 3.29x29 F110
3x33 3.33x33 Y114
3x37 3.37x37 Y118
TM4
4x53 4.53x53 V160
4x60 4.60x60 F167
ECL2
45x51 45.51x51 F182
45x52 45.52x52 A183
TM5
5x39 5.38x39 M198
5x43 5.42x43 A202
5x46 5.45x46 A205
TM6
6x58 6.58x58 Y266
TM7
7x34 7.35x34 H287
7x38 7.39x38 L291