PDB
9JCL
Resolution
2.8 Å
Released
Sept. 10, 2025
Receptor
P2Y1
Class
A
Species
Homo sapiens
Ligand
ADP
Function
Agonist
Reference
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Ligand Amino Acid Generic Number Segment Interaction Type
ADP L44 N-term hydrophobic
ADP Q50 1.31x31 TM1 polar (hydrogen bond)
ADP Q50 1.31x31 TM1 polar (hydrogen bond)
ADP Y110 2.63x63 TM2 polar (hydrogen bond)
ADP Y110 2.63x63 TM2 polar (hydrogen bond)
ADP Y111 2.64x64 TM2 Van der Waals
ADP Y111 2.64x64 TM2 polar (hydrogen bond)
ADP T115 ECL1 polar (hydrogen bond)
ADP T115 ECL1 Van der Waals
ADP R128 3.29x29 TM3 polar (charge-assisted hydrogen bond)
ADP R195 ECL2 polar (charge-assisted hydrogen bond)
ADP T201 ECL2 Van der Waals
ADP C202 45.50x50 ECL2 Van der Waals
ADP Y203 45.51x51 ECL2 hydrophobic
ADP Y203 45.51x51 ECL2 Van der Waals
ADP D204 45.52x52 ECL2 polar (hydrogen bond with backbone)
ADP D204 45.52x52 ECL2 Van der Waals
ADP T205 ECL2 Van der Waals
ADP T205 ECL2 polar (hydrogen bond)
ADP N283 6.58x58 TM6 polar (hydrogen bond)
ADP N283 6.58x58 TM6 polar (hydrogen bond)
ADP R287 6.62x62 TM6 polar (charge-assisted hydrogen bond)
ADP Q291 ECL3 Van der Waals
ADP N299 7.28x27 TM7 polar (hydrogen bond)
ADP N299 7.28x27 TM7 polar (hydrogen bond)
ADP Y303 7.32x31 TM7 hydrophobic
ADP Y303 7.32x31 TM7 Van der Waals
ADP Y306 7.35x34 TM7 Van der Waals
ADP R310 7.39x38 TM7 polar (charge-assisted hydrogen bond)

ADP

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

GPCRdb(A)
GPCRdb(A)
P2Y1 receptor
TM1
1x31 1.31x31 Q50
TM2
2x63 2.63x63 Y110
2x64 2.64x64 Y111
TM3
3x29 3.29x29 R128
ECL2
45x50 45.50x50 C202
45x51 45.51x51 Y203
45x52 45.52x52 D204
TM6
6x58 6.58x58 N283
6x62 6.62x62 R287
TM7
7x27 7.28x27 N299
7x31 7.32x31 Y303
7x34 7.35x34 Y306
7x38 7.39x38 R310