sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.410 Å
X-ray
2013-06-27
| Name: | Proto-oncogene tyrosine-protein kinase Src |
|---|---|
| ID: | SRC_CHICK |
| AC: | P00523 |
| Organism: | Gallus gallus |
| Reign: | Eukaryota |
| TaxID: | 9031 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.037 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.326 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.69 | 37.31 |
| According to VolSite | |
| HET Code: | VGG |
|---|---|
| Formula: | C17H21N5 |
| Molecular weight: | 295.382 g/mol |
| DrugBank ID: | DB08699 |
| Buried Surface Area: | 62.73 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -5.47105 | -7.26645 | -5.98977 |
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 |
| C22 | CB | LEU- 273 | 3.43 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 281 | 4.25 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 281 | 4.35 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 281 | 3.71 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 281 | 3.8 | 0 | Hydrophobic |
| C4 | CB | ALA- 293 | 4.46 | 0 | Hydrophobic |
| C16 | CB | ALA- 293 | 3.82 | 0 | Hydrophobic |
| C16 | CB | LYS- 295 | 3.7 | 0 | Hydrophobic |
| C18 | CE | MET- 314 | 3.84 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 323 | 4.3 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 336 | 4 | 0 | Hydrophobic |
| N10 | O | GLU- 339 | 2.95 | 172.31 | H-Bond (Ligand Donor) |
| N6 | N | MET- 341 | 3.18 | 169.5 | H-Bond (Protein Donor) |
| C21 | CD2 | LEU- 393 | 4.35 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 393 | 3.31 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 393 | 3.94 | 0 | Hydrophobic |
