sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2008-09-20
| 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: | 38.796 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.614 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 74.34 | 25.66 |
| According to VolSite | |
| HET Code: | PD3 |
|---|---|
| Formula: | C25H24F3N7O |
| Molecular weight: | 495.500 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.29 % |
| Polar Surface area: | 110.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 18.6075 | -5.75964 | 8.67047 |
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 |
| CAR | CB | LEU- 273 | 4.3 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 281 | 3.67 | 0 | Hydrophobic |
| C5 | CB | ALA- 293 | 4.1 | 0 | Hydrophobic |
| CAI | CD | LYS- 295 | 3.39 | 0 | Hydrophobic |
| CAF | CB | LYS- 295 | 3.38 | 0 | Hydrophobic |
| NAW | OE1 | GLU- 310 | 3.5 | 168.27 | H-Bond (Ligand Donor) |
| CAJ | CG | GLU- 310 | 3.32 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 313 | 4.01 | 0 | Hydrophobic |
| CAN | SD | MET- 314 | 3.81 | 0 | Hydrophobic |
| FAE | CG | MET- 314 | 4.45 | 0 | Hydrophobic |
| CBD | CG | MET- 314 | 3.88 | 0 | Hydrophobic |
| FAE | CD1 | LEU- 317 | 4.05 | 0 | Hydrophobic |
| FAE | CG | LEU- 322 | 3.93 | 0 | Hydrophobic |
| CAS | CG1 | VAL- 323 | 3.9 | 0 | Hydrophobic |
| NAA | O | GLU- 339 | 2.69 | 121.82 | H-Bond (Ligand Donor) |
| N1 | N | MET- 341 | 3.21 | 161.34 | H-Bond (Protein Donor) |
| CAQ | CB | SER- 345 | 4.47 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 393 | 3.73 | 0 | Hydrophobic |
| CAS | CG | LEU- 393 | 4.22 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 393 | 3.58 | 0 | Hydrophobic |
| FAD | CG1 | VAL- 402 | 3.9 | 0 | Hydrophobic |
| FAC | CG1 | VAL- 402 | 4.09 | 0 | Hydrophobic |
| CAS | CB | ALA- 403 | 4.45 | 0 | Hydrophobic |
| CAM | CB | ALA- 403 | 4.28 | 0 | Hydrophobic |
| CAN | CB | ASP- 404 | 3.72 | 0 | Hydrophobic |
| CAJ | CB | ASP- 404 | 3.82 | 0 | Hydrophobic |
| CAQ | CE1 | PHE- 405 | 4.07 | 0 | Hydrophobic |
