sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.570 Å
X-ray
2008-06-04
| 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 | 24 % |
| B | 76 % |
| B-Factor: | 42.581 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.900 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.92 | 41.08 |
| According to VolSite | |
| HET Code: | 25D |
|---|---|
| Formula: | C30H34N3O4 |
| Molecular weight: | 500.609 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.3 % |
| Polar Surface area: | 110.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 105.842 | -91.6331 | 92.5319 |
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 |
| C5 | CG1 | VAL- 40 | 4.05 | 0 | Hydrophobic |
| N7 | O | VAL- 40 | 3.06 | 144.97 | H-Bond (Ligand Donor) |
| C36 | CD | LYS- 41 | 3.98 | 0 | Hydrophobic |
| O9 | N | ASP- 42 | 2.82 | 170.32 | H-Bond (Protein Donor) |
| C14 | CB | ASP- 42 | 3.66 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 45 | 3.94 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 45 | 4.39 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 45 | 4.26 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 45 | 3.93 | 0 | Hydrophobic |
| C5 | CD2 | TRP- 67 | 4.04 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 68 | 4.06 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 68 | 4.16 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 68 | 4.24 | 0 | Hydrophobic |
| C12 | CB | GLN- 71 | 4.19 | 0 | Hydrophobic |
| C20 | CB | GLN- 71 | 3.58 | 0 | Hydrophobic |
| C4 | CG | GLN- 71 | 3.53 | 0 | Hydrophobic |
| C17 | CB | GLN- 72 | 4.26 | 0 | Hydrophobic |
| C14 | CB | GLN- 72 | 4 | 0 | Hydrophobic |
| C15 | CG | GLN- 72 | 3.65 | 0 | Hydrophobic |
| C17 | CB | TYR- 75 | 4.18 | 0 | Hydrophobic |
| C30 | CD1 | TYR- 75 | 3.55 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 155 | 4.09 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 193 | 3.9 | 18.59 | Pi/Cation |
| C25 | CZ | PHE- 196 | 3.88 | 0 | Hydrophobic |
| C36 | CE2 | PHE- 196 | 4.23 | 0 | Hydrophobic |
| C1 | CG2 | THR- 240 | 3.7 | 0 | Hydrophobic |
| C31 | CG | ARG- 310 | 4.05 | 0 | Hydrophobic |
| O33 | NE | ARG- 310 | 2.99 | 138.29 | H-Bond (Protein Donor) |
| O34 | NE | ARG- 310 | 3.44 | 144.58 | H-Bond (Protein Donor) |
| O33 | CZ | ARG- 310 | 3.77 | 0 | Ionic (Protein Cationic) |
| C29 | CB | ALA- 313 | 3.32 | 0 | Hydrophobic |
| O34 | O | HOH- 976 | 3.03 | 160.55 | H-Bond (Protein Donor) |
