sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 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 | 47 % |
| B | 53 % |
| B-Factor: | 27.078 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.033 | 1444.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.63 | 55.37 |
| According to VolSite | |
| HET Code: | FRX |
|---|---|
| Formula: | C20H19ClN4O4S |
| Molecular weight: | 446.907 g/mol |
| DrugBank ID: | DB07792 |
| Buried Surface Area: | 56.14 % |
| Polar Surface area: | 142.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 73.7558 | 13.7308 | 13.7735 |
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 |
| C15 | CG2 | THR- 38 | 4 | 0 | Hydrophobic |
| N11 | O | THR- 38 | 2.81 | 168.47 | H-Bond (Ligand Donor) |
| S2 | CD | ARG- 60 | 4.25 | 0 | Hydrophobic |
| CL | CB | ARG- 60 | 4.25 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 60 | 3.61 | 19.36 | Pi/Cation |
| CL | CB | LEU- 63 | 3.77 | 0 | Hydrophobic |
| CL | CG2 | VAL- 64 | 4.28 | 0 | Hydrophobic |
| CL | CE3 | TRP- 67 | 3.74 | 0 | Hydrophobic |
| C30 | CG | PRO- 188 | 4.09 | 0 | Hydrophobic |
| C29 | CB | PRO- 188 | 4.31 | 0 | Hydrophobic |
| N8 | O | GLU- 190 | 2.74 | 172.33 | H-Bond (Ligand Donor) |
| O19 | NZ | LYS- 191 | 2.52 | 133.69 | H-Bond (Protein Donor) |
| S2 | CB | LYS- 191 | 4.37 | 0 | Hydrophobic |
| C25 | CB | ALA- 192 | 3.61 | 0 | Hydrophobic |
| CL | CG | PRO- 229 | 4.29 | 0 | Hydrophobic |
