sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2011-02-02
| 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: | 44.772 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.645 | 1100.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.90 | 41.10 |
| According to VolSite | |
| HET Code: | PD5 |
|---|---|
| Formula: | C22H20F3N7O |
| Molecular weight: | 455.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.98 % |
| Polar Surface area: | 110.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 6.21755 | -33.9244 | -6.69664 |
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 |
| C5 | CG1 | VAL- 281 | 4.27 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 281 | 4.32 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 281 | 3.64 | 0 | Hydrophobic |
| C5 | CB | ALA- 293 | 3.98 | 0 | Hydrophobic |
| CAM | CD | LYS- 295 | 4.01 | 0 | Hydrophobic |
| CAP | CE | MET- 314 | 3.44 | 0 | Hydrophobic |
| CAY | SD | MET- 314 | 3.32 | 0 | Hydrophobic |
| CBA | CG | MET- 314 | 4.25 | 0 | Hydrophobic |
| FAF | CG2 | ILE- 317 | 3.8 | 0 | Hydrophobic |
| CBG | CD1 | ILE- 317 | 4.13 | 0 | Hydrophobic |
| FAF | CD1 | LEU- 322 | 4.32 | 0 | Hydrophobic |
| CAM | CG2 | THR- 338 | 4.03 | 0 | Hydrophobic |
| NAC | O | GLU- 339 | 2.87 | 157.04 | H-Bond (Ligand Donor) |
| N1 | N | MET- 341 | 2.79 | 174.51 | H-Bond (Protein Donor) |
| C5 | CD1 | LEU- 393 | 3.54 | 0 | Hydrophobic |
| CAB | CD2 | LEU- 393 | 3.93 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 393 | 3.55 | 0 | Hydrophobic |
| CAL | CB | ALA- 403 | 4.29 | 0 | Hydrophobic |
| CAL | CB | ASP- 404 | 3.61 | 0 | Hydrophobic |
| CAY | CB | ASP- 404 | 4.39 | 0 | Hydrophobic |
| OAD | N | ASP- 404 | 2.61 | 122.6 | H-Bond (Protein Donor) |
| CBG | CD2 | PHE- 405 | 3.71 | 0 | Hydrophobic |
| FAF | CE2 | PHE- 405 | 3.92 | 0 | Hydrophobic |
| FAG | CG | PHE- 405 | 3.96 | 0 | Hydrophobic |
| CAK | CD2 | PHE- 405 | 3.22 | 0 | Hydrophobic |
