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

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Ligand Amino Acid Generic Number Segment Interaction Type
AP503 S570 1.43x43 TM1 Van der Waals
AP503 C574 1.47x47 TM1 Van der Waals
AP503 L619 2.64x64 TM2 hydrophobic
AP503 F623 2.68x68 TM2 hydrophobic
AP503 L639 3.36x36 TM3 Van der Waals
AP503 H640 3.37x37 TM3 hydrophobic
AP503 F643 3.40x40 TM3 Van der Waals
AP503 F647 3.44x44 TM3 hydrophobic
AP503 W705 45.51x51 ECL2 aromatic (edge-to-face)
AP503 W705 45.51x51 ECL2 hydrophobic
AP503 L706 45.52x52 ECL2 hydrophobic
AP503 L708 ECL2 Van der Waals
AP503 I713 5.36x36 TM5 Van der Waals
AP503 F716 5.39x39 TM5 hydrophobic
AP503 F716 5.39x39 TM5 aromatic (edge-to-face)
AP503 V717 5.40x40 TM5 hydrophobic
AP503 A720 5.43x43 TM5 Van der Waals
AP503 L721 5.44x44 TM5 Van der Waals
AP503 W773 6.53x53 TM6 hydrophobic
AP503 G776 6.56x56 TM6 Van der Waals
AP503 V777 6.57x57 TM6 hydrophobic
AP503 F787 7.38x37 TM7 hydrophobic
AP503 F787 7.38x37 TM7 aromatic (edge-to-face)
AP503 Q788 7.39x38 TM7 Van der Waals
AP503 F791 7.42x41 TM7 hydrophobic
AP503 F791 7.42x41 TM7 aromatic (edge-to-face)
AP503 A792 7.43x42 TM7 Van der Waals
AP503 N795 7.46x45 TM7 polar (hydrogen bond)

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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
TM1
1x39 1.43x43 S570
1x43 1.47x47 C574
TM2
2x57 2.64x64 L619
2x61 2.68x68 F623
TM3
3x32 3.36x36 L639
3x33 3.37x37 H640
3x36 3.40x40 F643
3x40 3.44x44 F647
ECL2
45x51 45.51x51 W705
45x52 45.52x52 L706
TM5
5x40 5.36x36 I713
5x43 5.39x39 F716
5x44 5.40x40 V717
5x47 5.43x43 A720
5x48 5.44x44 L721
TM6
6x48 6.53x53 W773
6x51 6.56x56 G776
6x52 6.57x57 V777
TM7
7x33 7.38x37 F787
7x34 7.39x38 Q788
7x37 7.42x41 F791
7x38 7.43x42 A792
7x41 7.46x45 N795