sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2008-02-29
| 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 | 75 % |
| B | 25 % |
| B-Factor: | 28.130 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.345 | 2166.750 |
| % Hydrophobic | % Polar |
|---|---|
| 32.87 | 67.13 |
| According to VolSite | |
| HET Code: | AVE |
|---|---|
| Formula: | C16H7ClF5N2O5 |
| Molecular weight: | 437.682 g/mol |
| DrugBank ID: | DB07395 |
| Buried Surface Area: | 68.52 % |
| Polar Surface area: | 107.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 65.5374 | -12.0149 | 62.2561 |
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 |
| F11 | CB | VAL- 40 | 4.21 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 40 | 3.6 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 40 | 3.68 | 0 | Hydrophobic |
| C2 | CB | VAL- 40 | 3.68 | 0 | Hydrophobic |
| N12 | O | VAL- 40 | 2.76 | 163.68 | H-Bond (Ligand Donor) |
| C3 | CD | LYS- 41 | 4 | 0 | Hydrophobic |
| O27 | N | ASP- 42 | 3.18 | 152.96 | H-Bond (Protein Donor) |
| C17 | CB | ASN- 44 | 4.07 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 45 | 3.99 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 45 | 3.44 | 0 | Hydrophobic |
| CL10 | CD2 | TRP- 67 | 3.69 | 0 | Hydrophobic |
| F11 | CH2 | TRP- 67 | 3.31 | 0 | Hydrophobic |
| C6 | CZ2 | TRP- 67 | 3.46 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 68 | 3.59 | 0 | Hydrophobic |
| CL10 | CG | GLN- 71 | 3.38 | 0 | Hydrophobic |
| F31 | CB | GLN- 71 | 3.33 | 0 | Hydrophobic |
| C17 | CG | GLN- 72 | 3.57 | 0 | Hydrophobic |
| C18 | CG | GLN- 72 | 3.96 | 0 | Hydrophobic |
| F32 | CB | TYR- 75 | 3.21 | 0 | Hydrophobic |
| F34 | CG | LYS- 191 | 3.95 | 0 | Hydrophobic |
| F11 | CB | LYS- 191 | 3.22 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 193 | 3.96 | 37.3 | Pi/Cation |
| C2 | CD | ARG- 193 | 3.74 | 0 | Hydrophobic |
| F11 | CB | ASP- 227 | 3.65 | 0 | Hydrophobic |
