PDB
9V4D
Resolution
3.1 Å
Released
July 1, 2026
Receptor
C5a2
Class
A
Species
Homo sapiens
Ligand
R8Y
Function
Agonist
Reference
10.1016/J.MOLCEL.2026.06.002

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Ligand Amino Acid Generic Number Segment Interaction Type
R8Y L90 2.60x60 TM2 hydrophobic
R8Y W100 23.50x50 ECL1 hydrophobic
R8Y P111 3.29x29 TM3 hydrophobic
R8Y L115 3.33x33 TM3 hydrophobic
R8Y R173 ECL2 polar (charge-assisted hydrogen bond)
R8Y H176 ECL2 polar (hydrogen bond)
R8Y H176 ECL2 Van der Waals
R8Y Q185 ECL2 Van der Waals
R8Y C186 45.50x50 ECL2 Van der Waals
R8Y C186 45.50x50 ECL2 polar (hydrogen bond with backbone)
R8Y V187 45.51x51 ECL2 hydrophobic
R8Y V187 45.51x51 ECL2 Van der Waals
R8Y V188 45.52x52 ECL2 Van der Waals
R8Y V188 45.52x52 ECL2 polar (hydrogen bond with backbone)
R8Y D189 ECL2 polar (charge-assisted hydrogen bond)
R8Y E197 5.35x36 TM5 polar (charge-assisted hydrogen bond)
R8Y R204 5.42x43 TM5 polar (charge-assisted hydrogen bond)
R8Y Y249 6.51x51 TM6 polar (hydrogen bond)
R8Y Y249 6.51x51 TM6 aromatic (face-to-face)
R8Y Y249 6.51x51 TM6 polar (hydrogen bond with backbone)
R8Y L252 6.54x54 TM6 hydrophobic
R8Y L252 6.54x54 TM6 Van der Waals
R8Y G253 6.55x55 TM6 Van der Waals
R8Y L256 6.58x58 TM6 Van der Waals
R8Y L256 6.58x58 TM6 polar (hydrogen bond with backbone)
R8Y T257 6.59x59 TM6 polar (hydrogen bond with backbone)
R8Y T257 6.59x59 TM6 Van der Waals
R8Y A259 6.61x61 TM6 Van der Waals
R8Y A259 6.61x61 TM6 polar (hydrogen bond with backbone)
R8Y P261 ECL3 hydrophobic
R8Y P261 ECL3 Van der Waals
R8Y L266 7.28x27 TM7 hydrophobic
R8Y L266 7.28x27 TM7 Van der Waals
R8Y L270 7.32x31 TM7 hydrophobic
R8Y L270 7.32x31 TM7 Van der Waals
R8Y E273 7.35x34 TM7 polar (charge-assisted hydrogen bond)
R8Y V277 7.39x38 TM7 hydrophobic
R8Y V277 7.39x38 TM7 Van der Waals

R8Y

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

GPCRdb(A)
GPCRdb(A)
C5a2 receptor
TM2
2x60 2.60x60 L90
ECL1
23x50 23.50x50 W100
TM3
3x29 3.29x29 P111
3x33 3.33x33 L115
ECL2
45x50 45.50x50 C186
45x51 45.51x51 V187
45x52 45.52x52 V188
TM5
5x36 5.35x36 E197
5x43 5.42x43 R204
TM6
6x51 6.51x51 Y249
6x54 6.54x54 L252
6x55 6.55x55 G253
6x58 6.58x58 L256
6x59 6.59x59 T257
6x61 6.61x61 A259
TM7
7x27 7.28x27 L266
7x31 7.32x31 L270
7x34 7.35x34 E273
7x38 7.39x38 V277