PDB
9IYB
Resolution
2.8 Å
Released
Dec. 4, 2024
Receptor
DP2
Class
A
Species
Homo sapiens
Ligand
PGD2
Function
Agonist
Reference
—

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Ligand Amino Acid Generic Number Segment Interaction Type
PGD2 F87 2.60x60 TM2 hydrophobic
PGD2 F90 2.63x63 TM2 hydrophobic
PGD2 H107 3.28x28 TM3 polar (hydrogen bond)
PGD2 S108 3.29x29 TM3 Van der Waals
PGD2 F111 3.32x32 TM3 hydrophobic
PGD2 F111 3.32x32 TM3 Van der Waals
PGD2 F112 3.33x33 TM3 hydrophobic
PGD2 F112 3.33x33 TM3 Van der Waals
PGD2 R170 4.64x65 TM4 polar (charge-assisted hydrogen bond)
PGD2 I180 ECL2 polar (hydrogen bond with backbone)
PGD2 I180 ECL2 Van der Waals
PGD2 M181 ECL2 hydrophobic
PGD2 M181 ECL2 Van der Waals
PGD2 C182 45.50x50 ECL2 polar (hydrogen bond with backbone)
PGD2 C182 45.50x50 ECL2 polar (hydrogen bond)
PGD2 C182 45.50x50 ECL2 polar (hydrogen bond)
PGD2 Y183 45.51x51 ECL2 Van der Waals
PGD2 Y183 45.51x51 ECL2 hydrophobic
PGD2 Y184 45.52x52 ECL2 polar (hydrogen bond)
PGD2 Y184 45.52x52 ECL2 polar (hydrogen bond)
PGD2 Y262 6.51x51 TM6 polar (hydrogen bond)
PGD2 L286 7.35x34 TM7 hydrophobic
PGD2 L286 7.35x34 TM7 Van der Waals
PGD2 P287 7.36x35 TM7 Van der Waals
PGD2 T290 7.39x38 TM7 polar (hydrogen bond)
PGD2 F294 7.43x42 TM7 hydrophobic
PGD2 F294 7.43x42 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
DP2 receptor
TM2
2x60 2.60x60 F87
2x63 2.63x63 F90
TM3
3x28 3.28x28 H107
3x29 3.29x29 S108
3x32 3.32x32 F111
3x33 3.33x33 F112
TM4
4x65 4.64x65 R170
ECL2
45x50 45.50x50 C182
45x51 45.51x51 Y183
45x52 45.52x52 Y184
TM6
6x51 6.51x51 Y262
TM7
7x34 7.35x34 L286
7x35 7.36x35 P287
7x38 7.39x38 T290
7x42 7.43x42 F294