sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2000-05-04
| 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 | 42 % |
| B | 58 % |
| B-Factor: | 25.654 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.336 | 2180.250 |
| % Hydrophobic | % Polar |
|---|---|
| 33.90 | 66.10 |
| According to VolSite | |
| HET Code: | 700 |
|---|---|
| Formula: | C22H19ClN3O4 |
| Molecular weight: | 424.857 g/mol |
| DrugBank ID: | DB03744 |
| Buried Surface Area: | 63.56 % |
| Polar Surface area: | 105.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 90.8184 | 92.8878 | 70.6723 |
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 |
| C10 | CG2 | THR- 38 | 3.74 | 0 | Hydrophobic |
| N1 | O | THR- 38 | 3.2 | 156.28 | H-Bond (Ligand Donor) |
| C10 | CD1 | LEU- 39 | 4.43 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 40 | 3.53 | 0 | Hydrophobic |
| C12 | CB | PHE- 53 | 4.36 | 0 | Hydrophobic |
| C4 | CG | ARG- 60 | 3.43 | 0 | Hydrophobic |
| C3 | CD | ARG- 60 | 3.64 | 0 | Hydrophobic |
| CL1 | CB | LEU- 63 | 3.57 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 64 | 3.77 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 64 | 4.31 | 0 | Hydrophobic |
| CL1 | CE3 | TRP- 67 | 3.7 | 0 | Hydrophobic |
| C14 | CB | PRO- 188 | 3.67 | 0 | Hydrophobic |
| N2 | O | GLU- 190 | 2.73 | 165.28 | H-Bond (Ligand Donor) |
| O2 | NZ | LYS- 191 | 2.95 | 141.09 | H-Bond (Protein Donor) |
| C6 | CD | LYS- 191 | 4.35 | 0 | Hydrophobic |
| C1 | CB | LYS- 191 | 3.83 | 0 | Hydrophobic |
| C3 | CG | PRO- 229 | 3.9 | 0 | Hydrophobic |
