sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2000-03-16
| 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 | 51 % |
| B | 49 % |
| B-Factor: | 24.074 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.793 | 1589.625 |
| % Hydrophobic | % Polar |
|---|---|
| 28.87 | 71.13 |
| According to VolSite | |
| HET Code: | CP4 |
|---|---|
| Formula: | C24H24Cl2N4O4 |
| Molecular weight: | 503.378 g/mol |
| DrugBank ID: | DB02089 |
| Buried Surface Area: | 64.88 % |
| Polar Surface area: | 108.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -3.82232 | 34.2798 | 65.8488 |
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 |
| N11 | O | THR- 38 | 3.01 | 140.81 | H-Bond (Ligand Donor) |
| N21 | O | THR- 38 | 2.8 | 148.48 | H-Bond (Ligand Donor) |
| C14 | CG2 | THR- 38 | 3.96 | 0 | Hydrophobic |
| C19 | CG2 | THR- 38 | 3.87 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 40 | 3.4 | 0 | Hydrophobic |
| C30 | CG2 | VAL- 40 | 3.33 | 0 | Hydrophobic |
| C7 | CG | ARG- 60 | 3.38 | 0 | Hydrophobic |
| C32 | CG | ARG- 60 | 3.33 | 0 | Hydrophobic |
| C8 | CD | ARG- 60 | 3.51 | 0 | Hydrophobic |
| C30 | CD | ARG- 60 | 3.5 | 0 | Hydrophobic |
| CL10 | CB | LEU- 63 | 3.67 | 0 | Hydrophobic |
| CL33 | CB | LEU- 63 | 3.57 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 64 | 4.23 | 0 | Hydrophobic |
| CL10 | CG1 | VAL- 64 | 3.64 | 0 | Hydrophobic |
| CL33 | CG1 | VAL- 64 | 3.53 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 64 | 4.07 | 0 | Hydrophobic |
| CL10 | CE3 | TRP- 67 | 3.53 | 0 | Hydrophobic |
| CL33 | CE3 | TRP- 67 | 3.68 | 0 | Hydrophobic |
| N4 | O | GLU- 190 | 2.68 | 161.28 | H-Bond (Ligand Donor) |
| N25 | O | GLU- 190 | 2.81 | 165.83 | H-Bond (Ligand Donor) |
| C1 | CB | LYS- 191 | 3.71 | 0 | Hydrophobic |
| C27 | CB | LYS- 191 | 3.68 | 0 | Hydrophobic |
| C8 | CG | PRO- 229 | 3.82 | 0 | Hydrophobic |
| CL10 | CG | PRO- 229 | 4.24 | 0 | Hydrophobic |
| C31 | CG | PRO- 229 | 3.89 | 0 | Hydrophobic |
| CL33 | CG | PRO- 229 | 4.34 | 0 | Hydrophobic |
