PDB
9YDR
Resolution
2.1 Å
Released
Dec. 10, 2025
Receptor
δ
Class
A
Species
Homo sapiens
Ligands
Function
DADLE
Agonist
MIPS3983
PAM
Reference
—
DADLE MIPS3983

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Ligand Amino Acid Generic Number Segment Interaction Type
MIPS3983 L97 2.52x52 TM2 hydrophobic
DADLE Q105 2.60x60 TM2 hydrophobic
DADLE K108 2.63x63 TM2 hydrophobic
DADLE K108 2.63x63 TM2 polar (hydrogen bond)
DADLE W114 23.50x50 ECL1 hydrophobic
DADLE W114 23.50x50 ECL1 aromatic (edge-to-face)
MIPS3983 L119 3.23x23 TM3 hydrophobic
MIPS3983 K122 3.26x26 TM3 Van der Waals
MIPS3983 A123 3.27x27 TM3 hydrophobic
DADLE V124 3.28x28 TM3 hydrophobic
DADLE L125 3.29x29 TM3 hydrophobic
MIPS3983 S126 3.30x30 TM3 Van der Waals
MIPS3983 I127 3.31x31 TM3 hydrophobic
DADLE D128 3.32x32 TM3 polar (charge-charge)
DADLE Y129 3.33x33 TM3 hydrophobic
DADLE Y129 3.33x33 TM3 aromatic (edge-to-face)
MIPS3983 Y130 3.34x34 TM3 hydrophobic
MIPS3983 Y130 3.34x34 TM3 aromatic (face-to-face)
MIPS3983 N131 3.35x35 TM3 polar (hydrogen bond)
DADLE M132 3.36x36 TM3 hydrophobic
MIPS3983 W173 4.50x50 TM4 hydrophobic
MIPS3983 V174 4.51x51 TM4 Van der Waals
MIPS3983 S177 4.54x54 TM4 polar (hydrogen bond)
MIPS3983 V181 4.58x58 TM4 Van der Waals
MIPS3983 M184 4.61x61 TM4 hydrophobic
DADLE C198 45.50x50 ECL2 hydrophobic
DADLE K214 5.39x40 TM5 polar (charge-charge)
DADLE K214 5.39x40 TM5 polar (hydrogen bond)
DADLE V217 5.42x43 TM5 hydrophobic
DADLE W274 6.48x48 TM6 hydrophobic
DADLE I277 6.51x51 TM6 hydrophobic
DADLE H278 6.52x52 TM6 Van der Waals
DADLE V281 6.55x55 TM6 hydrophobic
DADLE W284 6.58x58 TM6 hydrophobic
DADLE L300 7.35x34 TM7 Van der Waals
DADLE I304 7.39x38 TM7 Van der Waals
DADLE Y308 7.43x42 TM7 polar (hydrogen bond)

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

GPCRdb(A)
GPCRdb(A)
δ receptor
TM2
2x52 2.52x52 L97
2x60 2.60x60 Q105
2x63 2.63x63 K108
ECL1
23x50 23.50x50 W114
TM3
3x23 3.23x23 L119
3x26 3.26x26 K122
3x27 3.27x27 A123
3x28 3.28x28 V124
3x29 3.29x29 L125
3x30 3.30x30 S126
3x31 3.31x31 I127
3x32 3.32x32 D128
3x33 3.33x33 Y129
3x34 3.34x34 Y130
3x35 3.35x35 N131
3x36 3.36x36 M132
TM4
4x50 4.50x50 W173
4x51 4.51x51 V174
4x54 4.54x54 S177
4x58 4.58x58 V181
4x61 4.61x61 M184
ECL2
45x50 45.50x50 C198
TM5
5x40 5.39x40 K214
5x43 5.42x43 V217
TM6
6x48 6.48x48 W274
6x51 6.51x51 I277
6x52 6.52x52 H278
6x55 6.55x55 V281
6x58 6.58x58 W284
TM7
7x34 7.35x34 L300
7x38 7.39x38 I304
7x42 7.43x42 Y308