PDB
7XZ5
Resolution
3.1 Å
Released
Aug. 24, 2022
Receptor
GPR119
Class
A
Species
Homo sapiens
Ligand
Lysophosphatidylcholine 18:1
Function
Agonist
Reference
10.1038/S41594-022-00816-5

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Ligand Amino Acid Generic Number Segment Interaction Type
Lysophosphatidylcholine 18:1 L61 2.60x60 TM2 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 Q65 2.64x64 TM2 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 Q65 2.64x64 TM2 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 M82 3.29x29 TM3 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 V85 3.32x32 TM3 Van der Waals
Lysophosphatidylcholine 18:1 T86 3.33x33 TM3 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 A89 3.36x36 TM3 hydrophobic
Lysophosphatidylcholine 18:1 A89 3.36x36 TM3 Van der Waals
Lysophosphatidylcholine 18:1 A90 3.37x37 TM3 Van der Waals
Lysophosphatidylcholine 18:1 A90 3.37x37 TM3 hydrophobic
Lysophosphatidylcholine 18:1 V93 3.40x40 TM3 Van der Waals
Lysophosphatidylcholine 18:1 V93 3.40x40 TM3 hydrophobic
Lysophosphatidylcholine 18:1 L94 3.41x41 TM3 Van der Waals
Lysophosphatidylcholine 18:1 L94 3.41x41 TM3 hydrophobic
Lysophosphatidylcholine 18:1 I136 4.56x56 TM4 Van der Waals
Lysophosphatidylcholine 18:1 C155 45.50x50 ECL2 Van der Waals
Lysophosphatidylcholine 18:1 C155 45.50x50 ECL2 polar (hydrogen bond with backbone)
Lysophosphatidylcholine 18:1 S156 45.51x51 ECL2 polar (hydrogen bond)
Lysophosphatidylcholine 18:1 S156 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
Lysophosphatidylcholine 18:1 F157 45.52x52 ECL2 polar (hydrogen bond with backbone)
Lysophosphatidylcholine 18:1 F157 45.52x52 ECL2 Van der Waals
Lysophosphatidylcholine 18:1 F158 ECL2 Van der Waals
Lysophosphatidylcholine 18:1 F158 ECL2 hydrophobic
Lysophosphatidylcholine 18:1 A159 ECL2 polar (hydrogen bond with backbone)
Lysophosphatidylcholine 18:1 A159 ECL2 Van der Waals
Lysophosphatidylcholine 18:1 L169 5.43x44 TM5 hydrophobic
Lysophosphatidylcholine 18:1 L169 5.43x44 TM5 Van der Waals
Lysophosphatidylcholine 18:1 G173 5.47x47 TM5 Van der Waals
Lysophosphatidylcholine 18:1 F174 5.48x48 TM5 Van der Waals
Lysophosphatidylcholine 18:1 F174 5.48x48 TM5 polar (hydrogen bond with backbone)
Lysophosphatidylcholine 18:1 W238 6.48x48 TM6 hydrophobic
Lysophosphatidylcholine 18:1 W238 6.48x48 TM6 Van der Waals
Lysophosphatidylcholine 18:1 F241 6.51x51 TM6 hydrophobic
Lysophosphatidylcholine 18:1 F241 6.51x51 TM6 Van der Waals
Lysophosphatidylcholine 18:1 Y257 7.31x30 TM7 Van der Waals
Lysophosphatidylcholine 18:1 E261 7.35x34 TM7 polar (charge-charge)
Lysophosphatidylcholine 18:1 E261 7.35x34 TM7 polar (charge-assisted hydrogen bond)
Lysophosphatidylcholine 18:1 E261 7.35x34 TM7 polar (hydrogen bond with backbone)
Lysophosphatidylcholine 18:1 R262 7.36x35 TM7 polar (charge-assisted hydrogen bond)
Lysophosphatidylcholine 18:1 W265 7.39x38 TM7 polar (hydrogen bond)

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ICL1 I H K N D ICL1ECL1 S P S ECL1ICL2 P F R Y L K I M ICL2ECL2 P M F Q Q T A Y K G Q C S F F A V ECL2ICL3 A M A G G Y ICL3ECL3 Q E C H L ECL3C-term G V K K V L T S F L L F L S A R N C G P E R P R E S S C H I V T I S S S E F D G C-term M E S S F S F G V I L A V L A S L I I A T N T L V A V A V L L L G V S L C F T L N L A V A D T L I G V A I S G L L T D Q L S R P T Q K T L C S L R M A F V T S S A A A S V L T V M L I T F D R Y L A I K Q S G F V A G A C I A G L W L V S Y L I G F L P L G I F H P H F V L T L S C V G F F P A M L L F V F F Y C D M L K I A S M H S Q Q I R K M E H A G R S P R T P S D F K A L R T V S V L I G S F A L S W T P F L I T G I V Q V A C Y L V L E R Y L W L L G V G N S L L N P L I Y A Y W Q K E L Y H V R L Q M A L
Helix box plot — Download: PNG | SVG T N T A I I L S A L V A L I V G F S F S 1 L N L A V A D T L I G V A I S G L L T D 2 L M V T L V S A A A S S T V F A M R L S 3 A G A C I A G L W L V S Y L I G F L P L 4 F F V F L L M A P F F G V C S L T L V F H 5 S V L I G S F A L S W T P F L I T G I V 6 L P N L L S N G V G L L W L Y R E L V 7

GPCRdb(A)
GPCRdb(A)
GPR119
TM2
2x60 2.60x60 L61
2x64 2.64x64 Q65
TM3
3x29 3.29x29 M82
3x32 3.32x32 V85
3x33 3.33x33 T86
3x36 3.36x36 A89
3x37 3.37x37 A90
3x40 3.40x40 V93
3x41 3.41x41 L94
TM4
4x56 4.56x56 I136
ECL2
45x50 45.50x50 C155
45x51 45.51x51 S156
45x52 45.52x52 F157
TM5
5x44 5.43x44 L169
5x47 5.47x47 G173
5x48 5.48x48 F174
TM6
6x48 6.48x48 W238
6x51 6.51x51 F241
TM7
7x30 7.31x30 Y257
7x34 7.35x34 E261
7x35 7.36x35 R262
7x38 7.39x38 W265