PDB
8X9T
Resolution
2.8 Å
Released
Feb. 12, 2025
Receptor
ADGRD1
Class
B2
Species
Homo sapiens
Ligand
AP503
Function
Agonist
Reference
10.1016/J.CELL.2025.01.006

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Ligand Amino Acid Generic Number Segment Interaction Type
AP503 L619 2.64x64 TM2 hydrophobic
AP503 F623 2.68x68 TM2 hydrophobic
AP503 F643 3.40x40 TM3 hydrophobic
AP503 F647 3.44x44 TM3 hydrophobic
AP503 W705 45.51x51 ECL2 aromatic (face-to-edge)
AP503 L706 45.52x52 ECL2 hydrophobic
AP503 F716 5.39x39 TM5 aromatic (edge-to-face)
AP503 V717 5.40x40 TM5 hydrophobic
AP503 W773 6.53x53 TM6 hydrophobic
AP503 V777 6.57x57 TM6 hydrophobic
AP503 F787 7.38x37 TM7 hydrophobic
AP503 F791 7.42x41 TM7 aromatic (face-to-edge)
AP503 N795 7.46x45 TM7 polar (hydrogen bond)
AP503 N795 7.46x45 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(B)
ADGRD1
TM2
2x57 2.64x64 L619
2x61 2.68x68 F623
TM3
3x36 3.40x40 F643
3x40 3.44x44 F647
ECL2
45x51 45.51x51 W705
45x52 45.52x52 L706
TM5
5x43 5.39x39 F716
5x44 5.40x40 V717
TM6
6x48 6.53x53 W773
6x52 6.57x57 V777
TM7
7x33 7.38x37 F787
7x37 7.42x41 F791
7x41 7.46x45 N795