δ receptor - Gi1

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Homo sapiens

GPCR PREFERRED CHAIN

R

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Homo sapiens

PDB CODE

9YDP

RESOLUTION

2.0 Å

REFERENCE

10.1101/2025.10.16.682975

PUBLICATION DATE

Dec. 10, 2025

3D VIEW

NGL is a WebGL based 3D viewer powered by MMTF.

LIGAND INTERACTIONS

46 interactions (Click to see)

LIGANDS

DADLE - Agonist pubchem gtoplig chembl_ligand drugbank pubchem

PHYSIOLOGICAL LIGANDS

[Met]enkephalin (Human), dynorphin A (Human), dynorphin A-(1-8) (Human), dynorphin A-(1-13) (Human), β-endorphin (Mouse), endomorphin-1 (Human), β-endorphin (Rat), dynorphin B (Human), β-endorphin (Human), α-neoendorphin (Human), [Leu]enkephalin (Human)



GPCR - G protein interface interactions



The biflare plot is a modified version of a flareplot, where lines are drawn between an inner concentric circle (Gα residues) and an outer concentric circle (GPCR residues) depicting the interface interactions.
Different interaction types are shown with different line types (aromatic - solid, hydrophobic - dashed, ionic - long dashed, polar - dotted, Van der Waals - dash-dot).
The interactive features include filtering on interaction type, segments, residues and backbone or sidechain interactions.


Interaction definitions:

Residue numbering:

GPCR-G protein backbone (bb) or sidechain (sc):





Structures

Sequence Color

Gα, Gβ, Gγ, GPCR
Interaction cut-off: strict (stick), loose (line)

NGL is a WebGL based 3D viewer powered by MMTF.

Interaction
type		 GPCR
Segment
AA
Number		 Generic
number		 Gα
segment
AA
Number		 Generic
number
Polar ICL3 R 244 - G.H5 K 232 G.H5.17
Hydrophobic ICL3 R 244 - G.H5 K 232 G.H5.17
Van-der-waals ICL3 R 244 - G.H5 K 232 G.H5.17
Hydrophobic TM5 L 240 5x65 G.H5 L 235 G.H5.20
Van-der-waals TM5 L 240 5x65 G.H5 L 235 G.H5.20
Hydrophobic ICL2 P 153 34x50 G.H5 I 231 G.H5.16
Van-der-waals ICL2 P 153 34x50 G.H5 I 231 G.H5.16
Hydrophobic TM3 V 150 3x54 G.H5 I 231 G.H5.16
Van-der-waals TM3 V 150 3x54 G.H5 I 231 G.H5.16
Hydrophobic TM3 R 146 3x50 G.H5 L 240 G.H5.25
Van-der-waals TM3 R 146 3x50 G.H5 L 240 G.H5.25
Polar ICL2 P 153 34x50 G.H5 N 234 G.H5.19
Van-der-waals ICL2 P 153 34x50 G.H5 N 234 G.H5.19
Hydrophobic ICL3 L 246 - G.h4s6 G 202 G.h4s6.11
Van-der-waals ICL3 L 246 - G.h4s6 G 202 G.h4s6.11
Polar H8 E 323 8x48 G.H5 G 239 G.H5.24
Hydrophobic H8 E 323 8x48 G.H5 G 239 G.H5.24
Van-der-waals H8 E 323 8x48 G.H5 G 239 G.H5.24
Hydrophobic ICL3 L 245 - G.H5 K 232 G.H5.17
Hydrophobic ICL2 P 153 34x50 G.H5 T 227 G.H5.12
Hydrophobic TM5 R 239 5x64 G.H5 I 231 G.H5.16
Van-der-waals TM5 R 239 5x64 G.H5 I 231 G.H5.16
Hydrophobic H8 E 323 8x48 G.H5 F 241 G.H5.26
Polar H8 N 324 8x49 G.H5 D 237 G.H5.22
Van-der-waals H8 N 324 8x49 G.H5 D 237 G.H5.22
Hydrophobic ICL2 A 156 34x53 G.H5 N 234 G.H5.19
Van-der-waals ICL2 A 156 34x53 G.H5 N 234 G.H5.19
Polar H8 R 327 8x52 G.H5 F 241 G.H5.26
Aromatic H8 R 327 8x52 G.H5 F 241 G.H5.26
Hydrophobic H8 R 327 8x52 G.H5 F 241 G.H5.26
Van-der-waals H8 R 327 8x52 G.H5 F 241 G.H5.26
Ionic ICL3 R 244 - G.H5 D 225 G.H5.10
Hydrophobic TM6 M 262 6x36 G.H5 L 240 G.H5.25
Van-der-waals TM6 M 262 6x36 G.H5 L 240 G.H5.25
Polar TM2 T 84 2x39 G.H5 D 237 G.H5.22
Van-der-waals TM2 T 84 2x39 G.H5 D 237 G.H5.22
Polar TM3 A 149 3x53 G.H5 N 234 G.H5.19
Hydrophobic TM3 A 149 3x53 G.H5 N 234 G.H5.19
Van-der-waals TM3 A 149 3x53 G.H5 N 234 G.H5.19
Hydrophobic ICL3 L 245 - G.H5 L 235 G.H5.20
Van-der-waals ICL3 L 245 - G.H5 L 235 G.H5.20
Hydrophobic ICL3 L 246 - G.H5 F 241 G.H5.26
Hydrophobic TM6 I 259 6x33 G.H5 L 240 G.H5.25
Van-der-waals TM6 I 259 6x33 G.H5 L 240 G.H5.25
Hydrophobic ICL3 S 247 - G.h4s6 T 197 G.h4s6.03
Van-der-waals ICL3 S 247 - G.h4s6 T 197 G.h4s6.03
Hydrophobic TM3 A 149 3x53 G.H5 C 238 G.H5.23
Van-der-waals TM3 A 149 3x53 G.H5 C 238 G.H5.23
Polar H8 N 324 8x49 G.H5 R 236 G.H5.21
Hydrophobic H8 N 324 8x49 G.H5 R 236 G.H5.21
Van-der-waals H8 N 324 8x49 G.H5 R 236 G.H5.21
Hydrophobic H8 N 324 8x49 G.H5 G 239 G.H5.24
Van-der-waals H8 N 324 8x49 G.H5 G 239 G.H5.24
Hydrophobic TM5 V 243 5x68 G.H5 D 228 G.H5.13
Van-der-waals TM5 V 243 5x68 G.H5 D 228 G.H5.13
Hydrophobic ICL2 V 154 34x51 G.S3 V 74 G.S3.01
Van-der-waals ICL2 V 154 34x51 G.S3 V 74 G.S3.01
Polar TM3 D 145 3x49 G.H5 C 238 G.H5.23
Ionic ICL2 R 160 34x57 G.H5 D 237 G.H5.22
Polar ICL2 R 160 34x57 G.H5 D 237 G.H5.22
Hydrophobic ICL2 R 160 34x57 G.H5 D 237 G.H5.22
Van-der-waals ICL2 R 160 34x57 G.H5 D 237 G.H5.22
Hydrophobic ICL2 L 157 34x54 G.H5 I 230 G.H5.15
Hydrophobic TM5 V 243 5x68 G.H5 I 231 G.H5.16
Van-der-waals TM5 V 243 5x68 G.H5 I 231 G.H5.16
Hydrophobic ICL3 L 246 - G.h4s6 D 201 G.h4s6.10
Van-der-waals ICL3 L 246 - G.h4s6 D 201 G.h4s6.10
Ionic ICL2 D 158 34x55 G.hns1 R 27 G.hns1.03
Hydrophobic TM3 V 150 3x54 G.H5 L 235 G.H5.20
Van-der-waals TM3 V 150 3x54 G.H5 L 235 G.H5.20
Hydrophobic ICL2 P 153 34x50 G.H5 I 230 G.H5.15
Van-der-waals ICL2 P 153 34x50 G.H5 I 230 G.H5.15
Hydrophobic H8 D 322 8x47 G.H5 G 239 G.H5.24
Van-der-waals H8 D 322 8x47 G.H5 G 239 G.H5.24
Polar ICL2 D 158 34x55 G.hns1 R 27 G.hns1.03
Polar ICL2 R 160 34x57 G.H5 C 238 G.H5.23
Polar TM2 T 84 2x39 G.H5 C 238 G.H5.23
Hydrophobic TM2 T 84 2x39 G.H5 C 238 G.H5.23
Van-der-waals TM2 T 84 2x39 G.H5 C 238 G.H5.23
Hydrophobic TM5 L 240 5x65 G.H5 I 231 G.H5.16
Hydrophobic ICL2 R 160 34x57 G.H5 C 238 G.H5.23
Van-der-waals ICL2 R 160 34x57 G.H5 C 238 G.H5.23
Hydrophobic TM5 V 243 5x68 G.H5 K 232 G.H5.17
Hydrophobic H8 E 323 8x48 G.H5 L 240 G.H5.25
Polar TM6 R 258 6x32 G.H5 L 240 G.H5.25
Hydrophobic TM6 R 258 6x32 G.H5 L 240 G.H5.25
Van-der-waals TM6 R 258 6x32 G.H5 L 240 G.H5.25
Hydrophobic ICL2 V 154 34x51 G.H5 I 230 G.H5.15
Polar ICL3 S 247 - G.h4s6 D 201 G.h4s6.10
Van-der-waals ICL3 S 247 - G.h4s6 D 201 G.h4s6.10
Hydrophobic TM5 M 236 5x61 G.H5 L 240 G.H5.25
Hydrophobic H8 R 327 8x52 G.H5 R 236 G.H5.21
Van-der-waals H8 R 327 8x52 G.H5 R 236 G.H5.21
Van-der-waals TM5 M 236 5x61 G.H5 L 240 G.H5.25
Hydrophobic ICL3 R 244 - G.S6 Y 207 G.S6.02
Van-der-waals ICL3 R 244 - G.S6 Y 207 G.S6.02
Hydrophobic ICL3 L 245 - G.H5 F 241 G.H5.26
Van-der-waals ICL3 L 245 - G.H5 F 241 G.H5.26
Ionic ICL3 R 244 - G.H5 D 228 G.H5.13
Polar ICL3 R 244 - G.H5 D 228 G.H5.13
Hydrophobic TM6 R 258 6x32 G.H5 F 241 G.H5.26
Van-der-waals TM6 R 258 6x32 G.H5 F 241 G.H5.26
Hydrophobic TM6 I 259 6x33 G.H5 F 241 G.H5.26
Polar ICL2 R 160 34x57 G.H5 N 234 G.H5.19
Hydrophobic TM6 S 255 6x29 G.H5 F 241 G.H5.26
Hydrophobic TM3 R 146 3x50 G.H5 C 238 G.H5.23
Van-der-waals TM3 R 146 3x50 G.H5 C 238 G.H5.23
Hydrophobic TM2 T 82 2x37 G.H5 D 237 G.H5.22
Van-der-waals TM2 T 82 2x37 G.H5 D 237 G.H5.22