sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-04-04
| Name: | Proto-oncogene tyrosine-protein kinase Src |
|---|---|
| ID: | SRC_HUMAN |
| AC: | P12931 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 40.557 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.247 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 55.60 | 44.40 |
| According to VolSite | |
| HET Code: | 0J9 |
|---|---|
| Formula: | C19H19N5 |
| Molecular weight: | 317.388 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.28 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 19.4539 | 23.7927 | 57.4353 |
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 |
| CAB | CB | LEU- 273 | 3.41 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 281 | 4 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 281 | 4.25 | 0 | Hydrophobic |
| CAB | CG1 | VAL- 281 | 3.87 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 281 | 3.75 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 281 | 4.37 | 0 | Hydrophobic |
| CAF | CB | ALA- 293 | 3.3 | 0 | Hydrophobic |
| CAK | CD | LYS- 295 | 4.19 | 0 | Hydrophobic |
| CAE | CB | LYS- 295 | 3.82 | 0 | Hydrophobic |
| CAJ | CG2 | ILE- 336 | 3.99 | 0 | Hydrophobic |
| NAD | O | GLU- 339 | 2.69 | 156.36 | H-Bond (Ligand Donor) |
| N1 | N | MET- 341 | 2.87 | 166.38 | H-Bond (Protein Donor) |
| CAC | CB | SER- 345 | 4 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 393 | 3.57 | 0 | Hydrophobic |
| CAC | CD2 | LEU- 393 | 4.23 | 0 | Hydrophobic |
| CAI | CD1 | LEU- 393 | 3.88 | 0 | Hydrophobic |
| CAG | CB | ALA- 403 | 3.59 | 0 | Hydrophobic |
| CAG | CB | ASP- 404 | 4.3 | 0 | Hydrophobic |
