Research workbench
Design of inhibitors of glycogen phosphorylase: a study of alpha-and beta-C-glucosides and 1-thio-beta-D-glucose compounds
Analyse Design of inhibitors of glycogen phosphorylase: a study of alpha-and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GG8
- Type
- protein
- Length
- 830 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glycogen phosphorylase)
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- GLG, PLP, IMP
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (glycogen phosphorylase) (EC 2.4.1.1) | protein | 830 | 51% helix, 14% strand | P00489 |
Ligands and binding sites
- GLG · Alpha-D-glucopyranosyl-2-carboxylic acid amide · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- IMP · Inosinic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.84 | 0.95 | 49 | GLG, PLP |
| 2 | 149 | 0.80 | 0.96 | 43 | empty |
| 3 | 303 | 0.71 | 0.85 | 31 | empty |
| 4 | 184 | 0.55 | 0.79 | 24 | empty |
| 5 | 123 | 0.52 | 0.81 | 22 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1GG8 · Design of inhibitors of glycogen phosphorylase: a study of alpha-and beta-C-glucosides… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00489
- Elsewhere: RCSB PDB 1GG8 · PDBe 1GG8 · UniProt P00489
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