PDB
8J19
Resolution
3.2 Å
Released
June 21, 2023
Receptor
GPR84
Class
A
Species
Homo sapiens
Ligand
Function
6-nonylpyridine-2,4-diol
Agonist
Reference
10.1038/S41467-023-38985-6

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Ligand Amino Acid Generic Number Segment Interaction Type
6-nonylpyridine-2,4-diol L100 3.32x32 TM3 hydrophobic
6-nonylpyridine-2,4-diol F101 3.33x33 TM3 hydrophobic
6-nonylpyridine-2,4-diol N104 3.36x36 TM3 hydrophobic
6-nonylpyridine-2,4-diol I108 3.40x40 TM3 hydrophobic
6-nonylpyridine-2,4-diol F152 4.57x57 TM4 hydrophobic
6-nonylpyridine-2,4-diol V165 ECL2 hydrophobic
6-nonylpyridine-2,4-diol T167 ECL2 hydrophobic
6-nonylpyridine-2,4-diol S169 45.51x51 ECL2 polar (hydrogen bond)
6-nonylpyridine-2,4-diol R172 ECL2 polar (hydrogen bond)
6-nonylpyridine-2,4-diol L182 5.42x43 TM5 Van der Waals
6-nonylpyridine-2,4-diol M183 5.43x44 TM5 hydrophobic
6-nonylpyridine-2,4-diol Y186 5.46x461 TM5 hydrophobic
6-nonylpyridine-2,4-diol F335 6.51x51 TM6 hydrophobic
6-nonylpyridine-2,4-diol F335 6.51x51 TM6 aromatic (edge-to-face)
6-nonylpyridine-2,4-diol L336 6.52x52 TM6 Van der Waals
6-nonylpyridine-2,4-diol A356 7.39x38 TM7 hydrophobic
6-nonylpyridine-2,4-diol T359 7.42x41 TM7 hydrophobic
6-nonylpyridine-2,4-diol W360 7.43x42 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
GPR84
TM3
3x32 3.32x32 L100
3x33 3.33x33 F101
3x36 3.36x36 N104
3x40 3.40x40 I108
TM4
4x57 4.57x57 F152
ECL2
45x51 45.51x51 S169
TM5
5x43 5.42x43 L182
5x44 5.43x44 M183
5x461 5.46x461 Y186
TM6
6x51 6.51x51 F335
6x52 6.52x52 L336
TM7
7x38 7.39x38 A356
7x41 7.42x41 T359
7x42 7.43x42 W360