PDB
24XY
Resolution
3.0 Å
Released
June 10, 2026
Receptor
P2Y13
Class
A
Species
Homo sapiens
Ligand
ADP
Function
Agonist
Reference
10.1016/J.BBRC.2026.153976

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Ligand Amino Acid Generic Number Segment Interaction Type
ADP R38 N-term polar (charge-assisted hydrogen bond)
ADP C116 3.25x25 TM3 polar (hydrogen bond with backbone)
ADP C116 3.25x25 TM3 Van der Waals
ADP V121 3.30x30 TM3 Van der Waals
ADP Y124 3.33x33 TM3 aromatic (edge-to-face)
ADP Y124 3.33x33 TM3 polar (hydrogen bond)
ADP S175 4.57x57 TM4 Van der Waals
ADP N178 4.60x60 TM4 polar (hydrogen bond)
ADP N178 4.60x60 TM4 Van der Waals
ADP C194 45.50x50 ECL2 polar (hydrogen bond with backbone)
ADP C194 45.50x50 ECL2 Van der Waals
ADP K198 ECL2 polar (charge-assisted hydrogen bond)
ADP H206 5.36x36 TM5 Van der Waals
ADP V209 5.39x39 TM5 Van der Waals
ADP N210 5.40x40 TM5 polar (hydrogen bond)
ADP N210 5.40x40 TM5 polar (hydrogen bond)
ADP N210 5.40x40 TM5 Van der Waals
ADP C213 5.43x43 TM5 polar (hydrogen bond)
ADP R275 6.55x55 TM6 polar (charge-assisted hydrogen bond)
ADP Y278 6.58x58 TM6 polar (hydrogen bond)
ADP Q282 6.62x62 TM6 polar (hydrogen bond)
ADP Q282 6.62x62 TM6 Van der Waals
ADP K299 7.35x34 TM7 polar (charge-assisted hydrogen bond)

ADP

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

GPCRdb(A)
GPCRdb(A)
P2Y13 receptor
TM3
3x25 3.25x25 C116
3x30 3.30x30 V121
3x33 3.33x33 Y124
TM4
4x57 4.57x57 S175
4x60 4.60x60 N178
ECL2
45x50 45.50x50 C194
TM5
5x36 5.36x36 H206
5x39 5.39x39 V209
5x40 5.40x40 N210
5x43 5.43x43 C213
TM6
6x55 6.55x55 R275
6x58 6.58x58 Y278
6x62 6.62x62 Q282
TM7
7x34 7.35x34 K299