MolNFT v1 · #2828 · protein
Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site
1C8K · Protein (glycogen phosphorylase): “Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site”. X-ray diffraction, 2 ligands (PLP, CPB), 13 pockets (best druggability 0.84). MolNFT v1 #2828 on GenesisL1: 3D…
- PDB
- 1C8K
- 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
- PLP, CPB
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (glycogen phosphorylase) (EC 2.4.1.1) | protein | 830 | 51% helix, 15% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- CPB · 2-(2-chloro-phenyl)-5,7-dihydroxy-8-(3-hydroxy-1-methyl-piperidin-4-yl)-4H-benzopyran-4-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.84 | 0.96 | 50 | PLP |
| 2 | 157 | 0.80 | 0.96 | 42 | empty |
| 3 | 283 | 0.70 | 0.85 | 32 | empty |
| 4 | 171 | 0.54 | 0.80 | 25 | empty |
| 5 | 120 | 0.54 | 0.82 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1C8K · Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site · 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 1C8K · PDBe 1C8K · UniProt P00489
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