PDB
9K0K
Resolution
3.1 Å
Released
June 11, 2025
Receptor
P2Y4
Class
A
Species
Homo sapiens
Ligand
UTP
Function
Agonist
Reference
10.1038/S41421-025-00797-X

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Ligand Amino Acid Generic Number Segment Interaction Type
UTP D26 N-term polar (charge-assisted hydrogen bond)
UTP C27 N-term polar (hydrogen bond with backbone)
UTP C27 N-term Van der Waals
UTP W28 N-term Van der Waals
UTP W28 N-term hydrophobic
UTP F29 N-term aromatic (face-to-face)
UTP F29 N-term polar (hydrogen bond with backbone)
UTP F29 N-term Van der Waals
UTP K34 1.31x31 TM1 polar (charge-assisted hydrogen bond)
UTP Y94 2.63x63 TM2 polar (hydrogen bond)
UTP Y94 2.63x63 TM2 Van der Waals
UTP Y95 2.64x64 TM2 polar (hydrogen bond)
UTP Y95 2.64x64 TM2 polar (hydrogen bond)
UTP N99 ECL1 polar (hydrogen bond)
UTP N99 ECL1 Van der Waals
UTP H186 45.51x51 ECL2 Van der Waals
UTP D187 45.52x52 ECL2 polar (hydrogen bond with backbone)
UTP D187 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
UTP T188 ECL2 Van der Waals
UTP Y268 6.58x58 TM6 polar (hydrogen bond)
UTP Y268 6.58x58 TM6 Van der Waals
UTP R272 ECL3 polar (charge-assisted hydrogen bond)
UTP K289 7.36x35 TM7 Van der Waals
UTP R292 7.39x38 TM7 polar (charge-assisted hydrogen bond)

UTP

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

GPCRdb(A)
GPCRdb(A)
P2Y4 receptor
TM1
1x31 1.31x31 K34
TM2
2x63 2.63x63 Y94
2x64 2.64x64 Y95
ECL2
45x51 45.51x51 H186
45x52 45.52x52 D187
TM6
6x58 6.58x58 Y268
TM7
7x35 7.36x35 K289
7x38 7.39x38 R292