κ receptor - Gi1

GPCR CLASS (FAMILY)

Class A (Rhodopsin)

GPCR SPECIES

Homo sapiens

GPCR PREFERRED CHAIN

A

G PROTEIN (FAMILY)

Gi/o

G PROTEIN SPECIES

Homo sapiens

PDB CODE

9D61

RESOLUTION

3.6 Å

REFERENCE

10.1038/S41589-024-01812-0

PUBLICATION DATE

Jan. 15, 2025

3D VIEW

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

LIGAND INTERACTIONS

42 interactions (Click to see)

LIGANDS

JDTic - Inverse agonist pubchem gtoplig chembl_ligand chembl_ligand pubchem chembl_ligand pubchem

PHYSIOLOGICAL LIGANDS

[Met]enkephalin (Human), β-neoendorphin (Human), dynorphin A (Human), dynorphin A-(1-8) (Human), dynorphin A-(1-13) (Human), big dynorphin (Human), β-endorphin (Mouse), 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 TM6 K 265 6x26 G.h4s6 K 314 G.h4s6.08
Van-der-waals TM6 K 265 6x26 G.h4s6 K 314 G.h4s6.08
Hydrophobic TM2 T 92 2x37 G.H5 D 350 G.H5.22
Van-der-waals TM2 T 92 2x37 G.H5 D 350 G.H5.22
Hydrophobic ICL2 P 163 34x50 G.H5 I 343 G.H5.15
Van-der-waals ICL2 P 163 34x50 G.H5 I 343 G.H5.15
Hydrophobic TM3 V 160 3x54 G.H5 L 348 G.H5.20
Van-der-waals TM3 V 160 3x54 G.H5 L 348 G.H5.20
Hydrophobic TM4 T 171 4x38 G.HN E 28 G.HN.52
Van-der-waals TM4 T 171 4x38 G.HN E 28 G.HN.52
Polar ICL3 R 257 - G.H5 D 341 G.H5.13
Van-der-waals ICL3 R 257 - G.H5 D 341 G.H5.13
Hydrophobic ICL3 V 256 - G.H5 I 344 G.H5.16
Hydrophobic ICL3 L 258 - G.S6 Y 320 G.S6.02
Van-der-waals ICL3 L 258 - G.S6 Y 320 G.S6.02
Hydrophobic TM6 I 272 6x33 G.H5 F 354 G.H5.26
Polar ICL3 L 258 - G.H5 D 341 G.H5.13
Hydrophobic ICL3 L 258 - G.H5 D 341 G.H5.13
Hydrophobic ICL4 D 334 - G.H5 G 352 G.H5.24
Van-der-waals ICL4 D 334 - G.H5 G 352 G.H5.24
Hydrophobic ICL2 L 167 34x54 G.S3 L 194 G.S3.01
Polar TM3 A 159 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM3 A 159 3x53 G.H5 N 347 G.H5.19
Van-der-waals TM3 A 159 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM3 R 156 3x50 G.H5 L 353 G.H5.25
Ionic TM6 K 265 6x26 G.h4s6 E 318 G.h4s6.12
Hydrophobic TM5 L 253 5x65 G.H5 I 344 G.H5.16
Hydrophobic ICL2 V 164 34x51 G.S3 L 194 G.S3.01
Hydrophobic ICL2 P 163 34x50 G.H5 T 340 G.H5.12
Hydrophobic TM6 N 268 6x29 G.H5 F 354 G.H5.26
Hydrophobic TM3 V 160 3x54 G.H5 I 344 G.H5.16
Van-der-waals TM3 V 160 3x54 G.H5 I 344 G.H5.16
Hydrophobic ICL2 P 163 34x50 G.H5 I 344 G.H5.16
Van-der-waals ICL2 P 163 34x50 G.H5 I 344 G.H5.16
Ionic ICL2 D 168 34x55 G.hns1 R 32 G.hns1.03
Polar ICL2 D 168 34x55 G.hns1 R 32 G.hns1.03
Hydrophobic ICL2 D 168 34x55 G.hns1 R 32 G.hns1.03
Van-der-waals ICL2 D 168 34x55 G.hns1 R 32 G.hns1.03
Hydrophobic TM6 I 272 6x33 G.H5 L 353 G.H5.25
Van-der-waals TM6 I 272 6x33 G.H5 L 353 G.H5.25
Polar H8 N 336 8x49 G.H5 D 350 G.H5.22
Van-der-waals H8 N 336 8x49 G.H5 D 350 G.H5.22
Ionic ICL2 R 170 34x57 G.H5 D 350 G.H5.22
Polar ICL2 R 170 34x57 G.H5 D 350 G.H5.22
Hydrophobic ICL2 R 170 34x57 G.H5 D 350 G.H5.22
Van-der-waals ICL2 R 170 34x57 G.H5 D 350 G.H5.22
Hydrophobic TM6 I 272 6x33 G.H5 L 348 G.H5.20
Hydrophobic ICL3 L 258 - G.h4s6 E 318 G.h4s6.12
Van-der-waals ICL3 L 258 - G.h4s6 E 318 G.h4s6.12
Hydrophobic TM5 L 253 5x65 G.H5 L 348 G.H5.20
Hydrophobic ICL2 V 164 34x51 G.s2s3 D 193 G.s2s3.02
Van-der-waals ICL2 V 164 34x51 G.s2s3 D 193 G.s2s3.02
Van-der-waals ICL3 L 258 - G.S5 S 263 G.S5.01
Polar TM6 R 271 6x32 G.H5 L 353 G.H5.25
Van-der-waals TM6 R 271 6x32 G.H5 L 353 G.H5.25
Hydrophobic TM5 R 252 5x64 G.H5 I 344 G.H5.16
Van-der-waals TM5 R 252 5x64 G.H5 I 344 G.H5.16
Hydrophobic TM6 L 275 6x36 G.H5 L 353 G.H5.25
Van-der-waals TM6 L 275 6x36 G.H5 L 353 G.H5.25
Hydrophobic ICL3 L 259 - G.H5 F 354 G.H5.26
Van-der-waals ICL3 L 259 - G.H5 F 354 G.H5.26
Polar H8 N 336 8x49 G.H5 C 351 G.H5.23
Hydrophobic ICL2 V 164 34x51 G.H5 I 343 G.H5.15
Hydrophobic H8 N 336 8x49 G.H5 G 352 G.H5.24
Polar ICL2 R 170 34x57 G.H5 C 351 G.H5.23
Hydrophobic ICL2 R 170 34x57 G.H5 C 351 G.H5.23
Van-der-waals ICL2 R 170 34x57 G.H5 C 351 G.H5.23
Polar TM3 D 155 3x49 G.H5 C 351 G.H5.23
Hydrophobic ICL3 L 258 - G.H5 K 345 G.H5.17
Van-der-waals ICL3 L 258 - G.H5 K 345 G.H5.17
Hydrophobic TM6 E 264 6x25 G.h4s6 D 315 G.h4s6.09
Van-der-waals TM6 E 264 6x25 G.h4s6 D 315 G.h4s6.09
Hydrophobic TM2 T 94 2x39 G.H5 C 351 G.H5.23
Hydrophobic ICL2 L 167 34x54 G.H5 I 343 G.H5.15
Polar ICL2 R 170 34x57 G.H5 N 347 G.H5.19
Ionic ICL3 R 257 - G.h4s6 E 318 G.h4s6.12
Polar ICL3 R 257 - G.h4s6 E 318 G.h4s6.12
Hydrophobic ICL3 R 257 - G.h4s6 E 318 G.h4s6.12
Hydrophobic ICL3 V 256 - G.H5 D 341 G.H5.13
Van-der-waals ICL3 V 256 - G.H5 D 341 G.H5.13
Hydrophobic ICL2 L 167 34x54 G.hns1 R 32 G.hns1.03
Hydrophobic ICL3 R 257 - G.S6 Y 320 G.S6.02
Van-der-waals ICL3 R 257 - G.S6 Y 320 G.S6.02