PDB
8XXV
Resolution
2.3 Å
Released
Dec. 4, 2024
Receptor
DP2
Class
A
Species
Homo sapiens
Ligands
indomethacin
Phosphatidylinositol (16:0/18:1)
Function
Agonist
PAM
Reference
—
indomethacin Phosphatidylinositol (16:0/18:1)

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Ligand Amino Acid Generic Number Segment Interaction Type
indomethacin F87 2.60x60 TM2 hydrophobic
indomethacin F111 3.32x32 TM3 hydrophobic
Phosphatidylinositol (16:0/18:1) F120 3.41x41 TM3 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) F120 3.41x41 TM3 Van der Waals
Phosphatidylinositol (16:0/18:1) S123 3.44x44 TM3 polar (hydrogen bond)
Phosphatidylinositol (16:0/18:1) A124 3.45x45 TM3 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) A124 3.45x45 TM3 Van der Waals
Phosphatidylinositol (16:0/18:1) L127 3.48x48 TM3 Van der Waals
Phosphatidylinositol (16:0/18:1) L127 3.48x48 TM3 hydrophobic
Phosphatidylinositol (16:0/18:1) D128 3.49x49 TM3 polar (charge-assisted hydrogen bond)
Phosphatidylinositol (16:0/18:1) D128 3.49x49 TM3 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) L131 3.52x52 TM3 Van der Waals
Phosphatidylinositol (16:0/18:1) W138 34.52x52 ICL2 polar (hydrogen bond)
Phosphatidylinositol (16:0/18:1) W138 34.52x52 ICL2 Van der Waals
Phosphatidylinositol (16:0/18:1) H142 34.56x56 ICL2 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) H142 34.56x56 ICL2 polar (hydrogen bond)
Phosphatidylinositol (16:0/18:1) R143 34.57x57 ICL2 Van der Waals
Phosphatidylinositol (16:0/18:1) T144 4.38x38 TM4 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) T144 4.38x38 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) A146 4.40x40 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) A147 4.41x41 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) A147 4.41x41 TM4 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) A148 4.42x42 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) K150 4.44x44 TM4 polar (charge-assisted hydrogen bond)
Phosphatidylinositol (16:0/18:1) V151 4.45x45 TM4 polar (hydrogen bond with backbone)
Phosphatidylinositol (16:0/18:1) V151 4.45x45 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) V154 4.48x48 TM4 hydrophobic
Phosphatidylinositol (16:0/18:1) V154 4.48x48 TM4 Van der Waals
Phosphatidylinositol (16:0/18:1) L155 4.49x49 TM4 hydrophobic
Phosphatidylinositol (16:0/18:1) L155 4.49x49 TM4 Van der Waals
indomethacin Y183 45.51x51 ECL2 aromatic (edge-to-face)
indomethacin Y184 45.52x52 ECL2 polar (hydrogen bond)
indomethacin Y262 6.51x51 TM6 polar (hydrogen bond)
indomethacin Y262 6.51x51 TM6 polar (hydrogen bond)
indomethacin L286 7.35x34 TM7 Van der Waals
indomethacin L286 7.35x34 TM7 hydrophobic
indomethacin P287 7.36x35 TM7 Van der Waals
indomethacin F294 7.43x42 TM7 Van der Waals
indomethacin F294 7.43x42 TM7 hydrophobic

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Download PDB file

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
TM3
3x32 3.32x32 F111
3x41 3.41x41 F120
3x44 3.44x44 S123
3x45 3.45x45 A124
3x48 3.48x48 L127
3x49 3.49x49 D128
3x52 3.52x52 L131
ICL2
34x52 34.52x52 W138
34x56 34.56x56 H142
34x57 34.57x57 R143
TM4
4x38 4.38x38 T144
4x40 4.40x40 A146
4x41 4.41x41 A147
4x42 4.42x42 A148
4x44 4.44x44 K150
4x45 4.45x45 V151
4x48 4.48x48 V154
4x49 4.49x49 L155
ECL2
45x51 45.51x51 Y183
45x52 45.52x52 Y184
TM6
6x51 6.51x51 Y262
TM7
7x34 7.35x34 L286
7x35 7.36x35 P287
7x42 7.43x42 F294