PDB
20ZX
Resolution
3.0 Å
Released
June 17, 2026
Receptor
LPA5
Class
A
Species
Homo sapiens
Ligand
LYSOPHOSPHATIDIC ACID
Function
Agonist
Reference
10.1073/PNAS.2537482123

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Ligand Amino Acid Generic Number Segment Interaction Type
LYSOPHOSPHATIDIC ACID M103 3.34x34 TM3 hydrophobic
LYSOPHOSPHATIDIC ACID Y106 3.37x37 TM3 hydrophobic
LYSOPHOSPHATIDIC ACID I110 3.41x41 TM3 hydrophobic
LYSOPHOSPHATIDIC ACID I149 4.53x53 TM4 hydrophobic
LYSOPHOSPHATIDIC ACID F152 4.56x56 TM4 hydrophobic
LYSOPHOSPHATIDIC ACID A156 4.60x61 TM4 hydrophobic
LYSOPHOSPHATIDIC ACID S178 ECL2 Van der Waals
LYSOPHOSPHATIDIC ACID S178 ECL2 polar (hydrogen bond with backbone)
LYSOPHOSPHATIDIC ACID F179 ECL2 hydrophobic
LYSOPHOSPHATIDIC ACID F179 ECL2 Van der Waals
LYSOPHOSPHATIDIC ACID W184 5.31x32 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID W184 5.31x32 TM5 polar (hydrogen bond)
LYSOPHOSPHATIDIC ACID L188 5.35x36 TM5 hydrophobic
LYSOPHOSPHATIDIC ACID L188 5.35x36 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID L191 5.38x39 TM5 hydrophobic
LYSOPHOSPHATIDIC ACID L191 5.38x39 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID V192 5.39x40 TM5 hydrophobic
LYSOPHOSPHATIDIC ACID V192 5.39x40 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID A195 5.42x43 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID A195 5.42x43 TM5 hydrophobic
LYSOPHOSPHATIDIC ACID L198 5.45x46 TM5 hydrophobic
LYSOPHOSPHATIDIC ACID L198 5.45x46 TM5 Van der Waals
LYSOPHOSPHATIDIC ACID L254 6.55x55 TM6 Van der Waals
LYSOPHOSPHATIDIC ACID Y257 6.58x58 TM6 polar (hydrogen bond)
LYSOPHOSPHATIDIC ACID R276 7.32x31 TM7 polar (charge-assisted hydrogen bond)
LYSOPHOSPHATIDIC ACID L279 7.35x34 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
LPA5 receptor
TM3
3x34 3.34x34 M103
3x37 3.37x37 Y106
3x41 3.41x41 I110
TM4
4x53 4.53x53 I149
4x56 4.56x56 F152
4x61 4.60x61 A156
TM5
5x32 5.31x32 W184
5x36 5.35x36 L188
5x39 5.38x39 L191
5x40 5.39x40 V192
5x43 5.42x43 A195
5x46 5.45x46 L198
TM6
6x55 6.55x55 L254
6x58 6.58x58 Y257
TM7
7x31 7.32x31 R276
7x34 7.35x34 L279