sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2005-08-25
| 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 | 69 % |
| B | 31 % |
| B-Factor: | 25.204 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.716 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 59.82 | 40.18 |
| According to VolSite | |
| HET Code: | IHU |
|---|---|
| Formula: | C15H12ClFN2O4 |
| Molecular weight: | 338.718 g/mol |
| DrugBank ID: | DB07968 |
| Buried Surface Area: | 72.6 % |
| Polar Surface area: | 87.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 33.1524 | 102.454 | 133.341 |
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 |
| N14 | O | VAL- 40 | 2.73 | 165.72 | H-Bond (Ligand Donor) |
| CL11 | CG1 | VAL- 40 | 4.31 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 40 | 3.68 | 0 | Hydrophobic |
| C6 | CB | VAL- 40 | 3.67 | 0 | Hydrophobic |
| C4 | CD | LYS- 41 | 3.95 | 0 | Hydrophobic |
| O55 | OD1 | ASP- 42 | 3.01 | 137.62 | H-Bond (Ligand Donor) |
| O16 | N | ASP- 42 | 3.44 | 132.73 | H-Bond (Protein Donor) |
| C22 | CB | ASN- 44 | 4.36 | 0 | Hydrophobic |
| O55 | ND2 | ASN- 44 | 3.15 | 161.5 | H-Bond (Protein Donor) |
| C19 | CG2 | VAL- 45 | 4.27 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 45 | 3.36 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 45 | 3.95 | 0 | Hydrophobic |
| F10 | CH2 | TRP- 67 | 3.54 | 0 | Hydrophobic |
| CL11 | CD2 | TRP- 67 | 3.65 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 68 | 4.11 | 0 | Hydrophobic |
| C51 | CB | GLN- 71 | 4.38 | 0 | Hydrophobic |
| CL11 | CG | GLN- 71 | 3.43 | 0 | Hydrophobic |
| C20 | CB | GLN- 72 | 3.88 | 0 | Hydrophobic |
| C21 | CG | GLN- 72 | 3.58 | 0 | Hydrophobic |
| C51 | CB | TYR- 75 | 4.2 | 0 | Hydrophobic |
| C20 | CB | TYR- 75 | 4.4 | 0 | Hydrophobic |
| C6 | CG | LYS- 191 | 4.46 | 0 | Hydrophobic |
| F10 | CB | LYS- 191 | 3.38 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 193 | 3.87 | 146.54 | Pi/Cation |
| F10 | CD | ARG- 193 | 3.63 | 0 | Hydrophobic |
| F10 | CB | ASP- 227 | 3.77 | 0 | Hydrophobic |
