succinate 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

8YKW

RESOLUTION

2.8 Å

REFERENCE

10.1038/S41422-024-00984-7

PUBLICATION DATE

May 29, 2024

3D VIEW

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

LIGAND INTERACTIONS

8 interactions (Click to see)

LIGANDS

succinic acid - Agonist pubchem gtoplig chembl_ligand drugbank drug_central pubchem

PHYSIOLOGICAL LIGANDS

succinic acid



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 cut-off:

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 L 225 - G.H5 K 345 G.H5.17
Hydrophobic TM6 L 227 6x30 G.H5 F 354 G.H5.26
Hydrophobic ICL2 P 127 - G.H5 I 343 G.H5.15
Van-der-waals ICL2 P 127 - G.H5 I 343 G.H5.15
Hydrophobic TM5 F 213 5x64 G.H5 I 344 G.H5.16
Van-der-waals TM5 F 213 5x64 G.H5 I 344 G.H5.16
Hydrophobic ICL3 V 221 - G.H5 D 337 G.H5.09
Hydrophobic TM6 L 233 6x36 G.H5 L 353 G.H5.25
Hydrophobic TM6 P 230 6x33 G.H5 F 354 G.H5.26
Van-der-waals TM6 P 230 6x33 G.H5 F 354 G.H5.26
Hydrophobic ICL3 A 224 - G.S6 Y 320 G.S6.02
Hydrophobic TM5 R 217 5x68 G.H5 T 340 G.H5.12
Hydrophobic ICL2 E 130 - G.hns1 R 32 G.hns1.03
Van-der-waals ICL2 E 130 - G.hns1 R 32 G.hns1.03
Polar TM3 R 120 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM3 R 120 3x50 G.H5 C 351 G.H5.23
Van-der-waals TM3 R 120 3x50 G.H5 C 351 G.H5.23
Hydrophobic TM6 V 234 6x37 G.H5 L 353 G.H5.25
Hydrophobic TM6 L 227 6x30 G.H5 L 348 G.H5.20
Hydrophobic ICL2 F 128 - G.hns1 A 31 G.hns1.02
Van-der-waals ICL2 F 128 - G.hns1 A 31 G.hns1.02
Ionic ICL2 R 129 - G.H5 D 350 G.H5.22
Polar ICL3 L 225 - G.h4s6 E 318 G.h4s6.12
Hydrophobic ICL3 L 225 - G.h4s6 E 318 G.h4s6.12
Van-der-waals ICL3 L 225 - G.h4s6 E 318 G.h4s6.12
Polar H8 G 299 8x47 G.H5 G 352 G.H5.24
Hydrophobic H8 G 299 8x47 G.H5 G 352 G.H5.24
Van-der-waals H8 G 299 8x47 G.H5 G 352 G.H5.24
Van-der-waals H8 H 301 8x49 G.H5 F 354 G.H5.26
Hydrophobic H8 F 302 8x50 G.H5 C 351 G.H5.23
Hydrophobic ICL3 V 221 - G.H5 F 334 G.H5.06
Van-der-waals ICL3 V 221 - G.H5 F 334 G.H5.06
Ionic H8 H 301 8x49 G.H5 D 350 G.H5.22
Polar TM6 K 229 6x32 G.H5 F 354 G.H5.26
Aromatic TM6 K 229 6x32 G.H5 F 354 G.H5.26
Hydrophobic ICL2 F 128 - G.S3 L 194 G.S3.01
Van-der-waals ICL2 F 128 - G.S3 L 194 G.S3.01
Hydrophobic ICL2 F 128 - G.H5 I 343 G.H5.15
Hydrophobic H8 D 300 8x48 G.H5 F 354 G.H5.26
Van-der-waals H8 D 300 8x48 G.H5 F 354 G.H5.26
Polar ICL2 P 127 - G.H5 N 347 G.H5.19
Hydrophobic ICL2 P 127 - G.H5 N 347 G.H5.19
Van-der-waals ICL2 P 127 - G.H5 N 347 G.H5.19
Hydrophobic H8 H 301 8x49 G.H5 K 349 G.H5.21
Van-der-waals H8 H 301 8x49 G.H5 K 349 G.H5.21
Hydrophobic ICL3 Q 220 - G.H5 D 337 G.H5.09
Van-der-waals ICL3 A 224 - G.h4s6 E 318 G.h4s6.12
Hydrophobic TM3 R 120 3x50 G.H5 L 353 G.H5.25
Polar ICL2 F 128 - G.hns1 R 32 G.hns1.03
Hydrophobic ICL2 F 128 - G.hns1 R 32 G.hns1.03
Polar TM3 I 123 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM3 I 123 3x53 G.H5 N 347 G.H5.19
Van-der-waals TM3 I 123 3x53 G.H5 N 347 G.H5.19
Hydrophobic TM2 S 58 2x39 G.H5 C 351 G.H5.23
Hydrophobic TM3 I 123 3x53 G.H5 C 351 G.H5.23
Van-der-waals TM3 I 123 3x53 G.H5 C 351 G.H5.23
Hydrophobic TM6 L 227 6x30 G.H5 K 345 G.H5.17
Hydrophobic H8 F 302 8x50 G.H5 D 350 G.H5.22
Van-der-waals H8 F 302 8x50 G.H5 D 350 G.H5.22
Hydrophobic ICL2 F 128 - G.S1 V 34 G.S1.02
Hydrophobic ICL3 V 221 - G.S6 Y 320 G.S6.02
Van-der-waals ICL3 V 221 - G.S6 Y 320 G.S6.02
Hydrophobic TM6 P 230 6x33 G.H5 L 348 G.H5.20
Polar ICL2 R 129 - G.hns1 R 32 G.hns1.03
Hydrophobic TM5 R 217 5x68 G.H5 I 344 G.H5.16
Polar TM6 P 230 6x33 G.H5 L 353 G.H5.25
Hydrophobic TM6 P 230 6x33 G.H5 L 353 G.H5.25
Van-der-waals TM6 P 230 6x33 G.H5 L 353 G.H5.25
Hydrophobic H8 F 302 8x50 G.H5 G 352 G.H5.24
Van-der-waals H8 F 302 8x50 G.H5 G 352 G.H5.24
Hydrophobic TM5 L 214 5x65 G.H5 L 348 G.H5.20