Crystal structure of glycogen phophorylase complexed with an anthranilimide based inhibitor GSK254

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).

Ligands and binding sites

• NBG · N-acetyl-beta-D-glucopyranosylamine · ligand · 2 copies · chains A, B
• PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
• CFF · Caffeine · ligand · 2 copies · chains A, B
• 25D · 2-cyclohexyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-D-alanine · ligand · 2 copies · chains A, B
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
• MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2637 Ų buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor, 1 modified (pyridoxal phosphate Schiff base, phosphorylation).

Compared structures

• 3DD1 · Crystal structure of glycogen phophorylase complexed with an anthranilimide based… · the same entry in another collection · chain A against A, TM-score 1.00
• P06737 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase, liver form (P06737) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P06737
• Elsewhere: RCSB PDB 3DD1 · PDBe 3DD1 · UniProt P06737