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
2006-09-19
| Name: | Glycogen phosphorylase, muscle form |
|---|---|
| ID: | PYGM_RABIT |
| AC: | P00489 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 2.4.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 35.367 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.280 | 2416.500 |
| % Hydrophobic | % Polar |
|---|---|
| 33.94 | 66.06 |
| According to VolSite | |
| HET Code: | FRY |
|---|---|
| Formula: | C18H15ClN4O3S |
| Molecular weight: | 402.855 g/mol |
| DrugBank ID: | DB07793 |
| Buried Surface Area: | 67.28 % |
| Polar Surface area: | 130.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 73.6984 | 50.352 | 52.09 |
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 |
| C14 | CG2 | THR- 38 | 3.83 | 0 | Hydrophobic |
| N11 | O | THR- 38 | 2.73 | 163.05 | H-Bond (Ligand Donor) |
| S2 | CD | ARG- 60 | 3.68 | 0 | Hydrophobic |
| CL | CG | ARG- 60 | 3.7 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 60 | 3.63 | 171.57 | Pi/Cation |
| CL | CB | LEU- 63 | 3.72 | 0 | Hydrophobic |
| CL | CG2 | VAL- 64 | 4.43 | 0 | Hydrophobic |
| CL | CE3 | TRP- 67 | 3.69 | 0 | Hydrophobic |
| C26 | CB | PRO- 188 | 3.91 | 0 | Hydrophobic |
| N8 | O | GLU- 190 | 2.74 | 160.3 | H-Bond (Ligand Donor) |
| S2 | CB | LYS- 191 | 4.33 | 0 | Hydrophobic |
| S2 | CG | PRO- 229 | 4.48 | 0 | Hydrophobic |
| CL | CG | PRO- 229 | 3.79 | 0 | Hydrophobic |
