sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.560 Å
X-ray
2007-07-13
| Name: | Glycogen phosphorylase, liver form |
|---|---|
| ID: | PYGL_HUMAN |
| AC: | P06737 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 61.962 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.986 | 1387.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.39 | 59.61 |
| According to VolSite | |
| HET Code: | PLP |
|---|---|
| Formula: | C8H8NO6P |
| Molecular weight: | 245.126 g/mol |
| DrugBank ID: | DB00114 |
| Buried Surface Area: | 60.26 % |
| Polar Surface area: | 132.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 25.7888 | 72.1908 | 35.2134 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C2A | CE2 | TYR- 90 | 3.63 | 0 | Hydrophobic |
| C4A | CG | ARG- 138 | 3.99 | 0 | Hydrophobic |
| C4 | CG | ARG- 138 | 4.11 | 0 | Hydrophobic |
| O3P | NZ | LYS- 568 | 3.16 | 172.54 | H-Bond (Protein Donor) |
| O3P | NZ | LYS- 568 | 3.16 | 0 | Ionic (Protein Cationic) |
| O1P | NZ | LYS- 574 | 3.46 | 125.25 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 574 | 3.46 | 0 | Ionic (Protein Cationic) |
| C2A | CE2 | TYR- 648 | 3.83 | 0 | Hydrophobic |
| C2A | CG2 | VAL- 650 | 4.09 | 0 | Hydrophobic |
| C2A | CB | ALA- 653 | 4.3 | 0 | Hydrophobic |
| C4 | CG2 | THR- 676 | 4.5 | 0 | Hydrophobic |
| C4A | CG2 | THR- 676 | 3.79 | 0 | Hydrophobic |
| C4 | CE | LYS- 680 | 4.07 | 0 | Hydrophobic |
| C4A | CD | LYS- 680 | 4.19 | 0 | Hydrophobic |
