PDB
8IRU
Resolution
3.2 Å
Released
June 21, 2023
Receptor
D4
Class
A
Species
Homo sapiens
Ligands
Cholesterol
rotigotine
Function
PAM
Agonist
Reference
10.1038/S41422-023-00808-0
Cholesterol rotigotine

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Ligand Amino Acid Generic Number Segment Interaction Type
Cholesterol A37 1.35x35 TM1 hydrophobic
Cholesterol G40 1.38x38 TM1 polar (hydrogen bond with backbone)
Cholesterol G40 1.38x38 TM1 Van der Waals
Cholesterol G41 1.39x39 TM1 Van der Waals
Cholesterol L43 1.41x41 TM1 Van der Waals
Cholesterol L44 1.42x42 TM1 polar (hydrogen bond with backbone)
Cholesterol L44 1.42x42 TM1 Van der Waals
Cholesterol A47 1.45x45 TM1 Van der Waals
rotigotine F91 2.61x60 TM2 aromatic (edge-to-face)
Cholesterol E95 2.65x64 TM2 polar (charge-assisted hydrogen bond)
rotigotine M112 3.29x29 TM3 polar (hydrogen bond)
rotigotine D115 3.32x32 TM3 polar (charge-assisted hydrogen bond)
rotigotine V116 3.33x33 TM3 Van der Waals
rotigotine V116 3.33x33 TM3 polar (hydrogen bond with backbone)
rotigotine C119 3.36x36 TM3 polar (hydrogen bond)
rotigotine T120 3.37x37 TM3 polar (hydrogen bond)
rotigotine C185 45.50x50 ECL2 Van der Waals
rotigotine C185 45.50x50 ECL2 polar (hydrogen bond with backbone)
rotigotine R186 45.51x51 ECL2 Van der Waals
rotigotine L187 45.52x52 ECL2 Van der Waals
rotigotine V193 5.39x40 TM5 Van der Waals
rotigotine S196 5.42x43 TM5 polar (hydrogen bond)
rotigotine S196 5.42x43 TM5 polar (hydrogen bond)
rotigotine S196 5.42x43 TM5 polar (hydrogen bond with backbone)
rotigotine S197 5.43x44 TM5 polar (hydrogen bond)
rotigotine S197 5.43x44 TM5 polar (hydrogen bond with backbone)
rotigotine S197 5.43x44 TM5 polar (hydrogen bond)
rotigotine S200 5.46x461 TM5 polar (hydrogen bond)
rotigotine W359 6.48x48 TM6 Van der Waals
rotigotine F362 6.51x51 TM6 Van der Waals
rotigotine F362 6.51x51 TM6 hydrophobic
rotigotine F363 6.52x52 TM6 aromatic (edge-to-face)
rotigotine F363 6.52x52 TM6 polar (hydrogen bond)
rotigotine H366 6.55x55 TM6 polar (hydrogen bond)
rotigotine H366 6.55x55 TM6 polar (hydrogen bond)
Cholesterol R380 7.33x32 TM7 Van der Waals
Cholesterol S383 7.36x35 TM7 polar (hydrogen bond)
Cholesterol S383 7.36x35 TM7 polar (hydrogen bond)
Cholesterol A384 7.37x36 TM7 Van der Waals
rotigotine T386 7.39x38 TM7 Van der Waals
rotigotine T386 7.39x38 TM7 polar (hydrogen bond with backbone)
Cholesterol W387 7.40x39 TM7 polar (hydrogen bond)
rotigotine G389 7.42x41 TM7 Van der Waals
rotigotine Y390 7.43x42 TM7 polar (hydrogen bond with backbone)
rotigotine Y390 7.43x42 TM7 polar (hydrogen bond)
Cholesterol V391 7.44x43 TM7 Van der Waals
Cholesterol A394 7.47x47 TM7 Van der Waals
Cholesterol L395 7.48x48 TM7 Van der Waals

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

GPCRdb(A)
GPCRdb(A)
D4 receptor
TM1
1x35 1.35x35 A37
1x38 1.38x38 G40
1x39 1.39x39 G41
1x41 1.41x41 L43
1x42 1.42x42 L44
1x45 1.45x45 A47
TM2
2x60 2.61x60 F91
2x64 2.65x64 E95
TM3
3x29 3.29x29 M112
3x32 3.32x32 D115
3x33 3.33x33 V116
3x36 3.36x36 C119
3x37 3.37x37 T120
ECL2
45x50 45.50x50 C185
45x51 45.51x51 R186
45x52 45.52x52 L187
TM5
5x40 5.39x40 V193
5x43 5.42x43 S196
5x44 5.43x44 S197
5x461 5.46x461 S200
TM6
6x48 6.48x48 W359
6x51 6.51x51 F362
6x52 6.52x52 F363
6x55 6.55x55 H366
TM7
7x32 7.33x32 R380
7x35 7.36x35 S383
7x36 7.37x36 A384
7x38 7.39x38 T386
7x39 7.40x39 W387
7x41 7.42x41 G389
7x42 7.43x42 Y390
7x43 7.44x43 V391
7x47 7.47x47 A394
7x48 7.48x48 L395