sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2002-03-07
| 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 | 54 % |
| B | 46 % |
| B-Factor: | 24.030 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.496 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.50 | 58.50 |
| According to VolSite | |
| HET Code: | 700 |
|---|---|
| Formula: | C22H19ClN3O4 |
| Molecular weight: | 424.857 g/mol |
| DrugBank ID: | DB03744 |
| Buried Surface Area: | 63.22 % |
| 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 |
|---|---|---|
| 65.1904 | -73.3945 | 78.0353 |
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 | 3.77 | 0 | Hydrophobic |
| N1 | O | THR- 38 | 3.19 | 152.51 | H-Bond (Ligand Donor) |
| C5 | CG2 | VAL- 40 | 3.56 | 0 | Hydrophobic |
| C12 | CB | PHE- 53 | 4.46 | 0 | Hydrophobic |
| C4 | CG | ARG- 60 | 3.4 | 0 | Hydrophobic |
| C3 | CD | ARG- 60 | 3.56 | 0 | Hydrophobic |
| CL1 | CB | LEU- 63 | 3.65 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 64 | 3.8 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 64 | 4.37 | 0 | Hydrophobic |
| CL1 | CE3 | TRP- 67 | 3.73 | 0 | Hydrophobic |
| C14 | CB | PRO- 188 | 3.49 | 0 | Hydrophobic |
| N2 | O | GLU- 190 | 2.78 | 168.77 | H-Bond (Ligand Donor) |
| O2 | NZ | LYS- 191 | 2.9 | 137.22 | H-Bond (Protein Donor) |
| C6 | CD | LYS- 191 | 4.36 | 0 | Hydrophobic |
| C1 | CB | LYS- 191 | 3.75 | 0 | Hydrophobic |
| C3 | CG | PRO- 229 | 3.92 | 0 | Hydrophobic |
| CL1 | CG | PRO- 229 | 4.39 | 0 | Hydrophobic |
