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
2008-06-06
| 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 | 23 % |
| B | 77 % |
| B-Factor: | 23.167 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.102 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.67 | 37.33 |
| According to VolSite | |
| HET Code: | 055 |
|---|---|
| Formula: | C27H21ClN3O4 |
| Molecular weight: | 486.926 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.21 % |
| Polar Surface area: | 110.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 106.168 | -92.0319 | 92.888 |
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 |
| C31 | CG1 | VAL- 40 | 3.82 | 0 | Hydrophobic |
| N24 | O | VAL- 40 | 3.02 | 159.65 | H-Bond (Ligand Donor) |
| CL1 | CD | LYS- 41 | 3.99 | 0 | Hydrophobic |
| O33 | N | ASP- 42 | 2.96 | 167.8 | H-Bond (Protein Donor) |
| C7 | CB | ASP- 42 | 3.69 | 0 | Hydrophobic |
| C8 | CB | ASN- 44 | 4.48 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 45 | 4.3 | 0 | Hydrophobic |
| C51 | CG1 | VAL- 45 | 4.34 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 45 | 3.71 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 45 | 4.03 | 0 | Hydrophobic |
| C31 | CD2 | TRP- 67 | 3.91 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 68 | 3.9 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 68 | 4.22 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 68 | 4.44 | 0 | Hydrophobic |
| C6 | CB | GLN- 71 | 4.2 | 0 | Hydrophobic |
| C4 | CB | GLN- 71 | 3.65 | 0 | Hydrophobic |
| C26 | CG | GLN- 71 | 3.63 | 0 | Hydrophobic |
| C8 | CG | GLN- 72 | 3.52 | 0 | Hydrophobic |
| C7 | CB | GLN- 72 | 3.84 | 0 | Hydrophobic |
| C10 | CB | TYR- 75 | 4.11 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 193 | 3.72 | 12.41 | Pi/Cation |
| CL1 | CE2 | PHE- 196 | 3.82 | 0 | Hydrophobic |
| C51 | CZ | PHE- 196 | 4.26 | 0 | Hydrophobic |
| C48 | CG | ARG- 309 | 4.06 | 0 | Hydrophobic |
| O21 | NE | ARG- 310 | 2.89 | 170.32 | H-Bond (Protein Donor) |
| O21 | NH2 | ARG- 310 | 3.36 | 137.34 | H-Bond (Protein Donor) |
| O21 | CZ | ARG- 310 | 3.59 | 0 | Ionic (Protein Cationic) |
| C47 | CG | ARG- 310 | 4.03 | 0 | Hydrophobic |
| C48 | CB | ARG- 310 | 4.49 | 0 | Hydrophobic |
| C48 | CB | ALA- 313 | 4.23 | 0 | Hydrophobic |
| O20 | O | HOH- 1022 | 2.89 | 126.02 | H-Bond (Protein Donor) |
| O21 | O | HOH- 1131 | 2.65 | 179.96 | H-Bond (Protein Donor) |
