PDB
8IRU
Resolution
3.2 Å
Released
June 21, 2023
Receptor
D4
Class
A
Species
Homo sapiens
Ligands
Function
Cholesterol
PAM
rotigotine
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 Van der Waals
Cholesterol G40 1.38x38 TM1 Van der Waals
Cholesterol L43 1.41x41 TM1 hydrophobic
Cholesterol L44 1.42x42 TM1 Van der Waals
Cholesterol A47 1.45x45 TM1 hydrophobic
Cholesterol C56 1.54x54 TM1 hydrophobic
Cholesterol V59 1.57x57 TM1 hydrophobic
Cholesterol A60 1.58x58 TM1 hydrophobic
Cholesterol Q66 12.51x51 ICL1 hydrophobic
Cholesterol Q66 12.51x51 ICL1 polar (hydrogen bond)
Cholesterol S71 2.41x41 TM2 polar (hydrogen bond)
Cholesterol V74 2.44x44 TM2 hydrophobic
Cholesterol S75 2.45x45 TM2 Van der Waals
Cholesterol A78 2.48x48 TM2 hydrophobic
Cholesterol L81 2.51x51 TM2 hydrophobic
Cholesterol L82 2.52x52 TM2 hydrophobic
Cholesterol L85 2.55x55 TM2 hydrophobic
Cholesterol L85 2.55x55 TM2 Van der Waals
Cholesterol L86 2.56x551 TM2 hydrophobic
Cholesterol L86 2.56x551 TM2 Van der Waals
Cholesterol L90 2.60x59 TM2 Van der Waals
rotigotine F91 2.61x60 TM2 hydrophobic
rotigotine F91 2.61x60 TM2 aromatic (edge-to-face)
Cholesterol L103 23.52x52 ECL1 hydrophobic
Cholesterol R106 3.23x23 TM3 hydrophobic
Cholesterol L107 3.24x24 TM3 hydrophobic
Cholesterol A110 3.27x27 TM3 hydrophobic
rotigotine M112 3.29x29 TM3 hydrophobic
Cholesterol M114 3.31x31 TM3 hydrophobic
rotigotine D115 3.32x32 TM3 polar (hydrogen bond)
rotigotine D115 3.32x32 TM3 polar (charge-charge)
rotigotine V116 3.33x33 TM3 hydrophobic
Cholesterol M117 3.34x34 TM3 hydrophobic
rotigotine C119 3.36x36 TM3 Van der Waals
rotigotine T120 3.37x37 TM3 Van der Waals
Cholesterol F124 3.41x41 TM3 hydrophobic
Cholesterol C127 3.44x44 TM3 hydrophobic
Cholesterol A128 3.45x45 TM3 Van der Waals
Cholesterol V131 3.48x48 TM3 hydrophobic
Cholesterol F134 3.51x51 TM3 hydrophobic
Cholesterol V135 3.52x52 TM3 Van der Waals
Cholesterol V139 3.56x56 TM3 Van der Waals
Cholesterol L155 4.45x45 TM4 hydrophobic
Cholesterol I156 4.46x46 TM4 hydrophobic
Cholesterol A158 4.48x48 TM4 Van der Waals
Cholesterol T159 4.49x49 TM4 Van der Waals
Cholesterol W160 4.50x50 TM4 hydrophobic
Cholesterol L162 4.52x52 TM4 hydrophobic
rotigotine C185 45.50x50 ECL2 Van der Waals
rotigotine L187 45.52x52 ECL2 hydrophobic
rotigotine S196 5.42x43 TM5 polar (hydrogen bond)
rotigotine S197 5.43x44 TM5 Van der Waals
rotigotine S200 5.46x461 TM5 Van der Waals
Cholesterol L207 5.53x53 TM5 hydrophobic
Cholesterol L357 6.46x46 TM6 hydrophobic
rotigotine W359 6.48x48 TM6 hydrophobic
Cholesterol P361 6.50x50 TM6 Van der Waals
rotigotine F362 6.51x51 TM6 hydrophobic
rotigotine F363 6.52x52 TM6 hydrophobic
rotigotine F363 6.52x52 TM6 aromatic (edge-to-face)
Cholesterol V364 6.53x53 TM6 hydrophobic
Cholesterol V364 6.53x53 TM6 Van der Waals
Cholesterol V365 6.54x54 TM6 hydrophobic
rotigotine H366 6.55x55 TM6 aromatic (pi-cation)
rotigotine H366 6.55x55 TM6 polar (hydrogen bond)
Cholesterol T368 6.57x57 TM6 Van der Waals
Cholesterol L371 6.60x60 TM6 hydrophobic
Cholesterol C372 6.61x61 TM6 hydrophobic
Cholesterol C375 ECL3 hydrophobic
Cholesterol S376 ECL3 Van der Waals
Cholesterol V377 ECL3 hydrophobic
Cholesterol P378 7.31x30 TM7 Van der Waals
Cholesterol R380 7.33x32 TM7 hydrophobic
Cholesterol L381 7.34x33 TM7 hydrophobic
Cholesterol S383 7.36x35 TM7 polar (hydrogen bond)
Cholesterol A384 7.37x36 TM7 hydrophobic
rotigotine T386 7.39x38 TM7 hydrophobic
Cholesterol W387 7.40x39 TM7 hydrophobic
Cholesterol L388 7.41x40 TM7 hydrophobic
rotigotine G389 7.42x41 TM7 Van der Waals
rotigotine Y390 7.43x42 TM7 hydrophobic
Cholesterol V391 7.44x43 TM7 Van der Waals
Cholesterol A394 7.47x47 TM7 hydrophobic
Cholesterol L395 7.48x48 TM7 hydrophobic

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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
1x41 1.41x41 L43
1x42 1.42x42 L44
1x45 1.45x45 A47
1x54 1.54x54 C56
1x57 1.57x57 V59
1x58 1.58x58 A60
ICL1
12x51 12.51x51 Q66
TM2
2x41 2.41x41 S71
2x44 2.44x44 V74
2x45 2.45x45 S75
2x48 2.48x48 A78
2x51 2.51x51 L81
2x52 2.52x52 L82
2x55 2.55x55 L85
2x551 2.56x551 L86
2x59 2.60x59 L90
2x60 2.61x60 F91
ECL1
23x52 23.52x52 L103
TM3
3x23 3.23x23 R106
3x24 3.24x24 L107
3x27 3.27x27 A110
3x29 3.29x29 M112
3x31 3.31x31 M114
3x32 3.32x32 D115
3x33 3.33x33 V116
3x34 3.34x34 M117
3x36 3.36x36 C119
3x37 3.37x37 T120
3x41 3.41x41 F124
3x44 3.44x44 C127
3x45 3.45x45 A128
3x48 3.48x48 V131
3x51 3.51x51 F134
3x52 3.52x52 V135
3x56 3.56x56 V139
TM4
4x45 4.45x45 L155
4x46 4.46x46 I156
4x48 4.48x48 A158
4x49 4.49x49 T159
4x50 4.50x50 W160
4x52 4.52x52 L162
ECL2
45x50 45.50x50 C185
45x52 45.52x52 L187
TM5
5x43 5.42x43 S196
5x44 5.43x44 S197
5x461 5.46x461 S200
5x53 5.53x53 L207
TM6
6x46 6.46x46 L357
6x48 6.48x48 W359
6x50 6.50x50 P361
6x51 6.51x51 F362
6x52 6.52x52 F363
6x53 6.53x53 V364
6x54 6.54x54 V365
6x55 6.55x55 H366
6x57 6.57x57 T368
6x60 6.60x60 L371
6x61 6.61x61 C372
TM7
7x30 7.31x30 P378
7x32 7.33x32 R380
7x33 7.34x33 L381
7x35 7.36x35 S383
7x36 7.37x36 A384
7x38 7.39x38 T386
7x39 7.40x39 W387
7x40 7.41x40 L388
7x41 7.42x41 G389
7x42 7.43x42 Y390
7x43 7.44x43 V391
7x47 7.47x47 A394
7x48 7.48x48 L395