PDB
9E9S
Resolution
2.7 Å
Released
Sept. 3, 2025
Receptor
DP1
Class
A
Species
Homo sapiens
Ligand
PGD2
Function
Agonist
Reference
10.1038/S41467-025-64002-Z

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Ligand Amino Acid Generic Number Segment Interaction Type
PGD2 K76 2.54x54 TM2 polar (charge-assisted hydrogen bond)
PGD2 L79 2.57x57 TM2 hydrophobic
PGD2 L79 2.57x57 TM2 Van der Waals
PGD2 S80 2.58x58 TM2 Van der Waals
PGD2 V83 2.61x61 TM2 hydrophobic
PGD2 V83 2.61x61 TM2 Van der Waals
PGD2 Y87 2.65x65 TM2 polar (hydrogen bond)
PGD2 Y87 2.65x65 TM2 Van der Waals
PGD2 M112 3.32x32 TM3 Van der Waals
PGD2 M112 3.32x32 TM3 hydrophobic
PGD2 F115 3.35x35 TM3 hydrophobic
PGD2 G116 3.36x36 TM3 Van der Waals
PGD2 T181 ECL2 Van der Waals
PGD2 T181 ECL2 polar (hydrogen bond)
PGD2 W182 ECL2 Van der Waals
PGD2 W182 ECL2 hydrophobic
PGD2 L306 7.36x35 TM7 Van der Waals
PGD2 L306 7.36x35 TM7 hydrophobic
PGD2 L309 7.39x38 TM7 hydrophobic
PGD2 L309 7.39x38 TM7 Van der Waals
PGD2 R310 7.40x39 TM7 polar (charge-assisted hydrogen bond)
PGD2 L312 7.42x41 TM7 hydrophobic
PGD2 L312 7.42x41 TM7 Van der Waals
PGD2 S313 7.43x42 TM7 Van der Waals
PGD2 S316 7.46x46 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
DP1 receptor
TM2
2x54 2.54x54 K76
2x57 2.57x57 L79
2x58 2.58x58 S80
2x61 2.61x61 V83
2x65 2.65x65 Y87
TM3
3x32 3.32x32 M112
3x35 3.35x35 F115
3x36 3.36x36 G116
TM7
7x35 7.36x35 L306
7x38 7.39x38 L309
7x39 7.40x39 R310
7x41 7.42x41 L312
7x42 7.43x42 S313
7x46 7.46x46 S316