sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2010-08-13
| 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: | 35.340 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.593 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 68.60 | 31.40 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 61.69 % |
| Polar Surface area: | 87.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -3.42138 | 33.0385 | -7.05468 |
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 |
| C6 | CD1 | LEU- 273 | 4.08 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 281 | 3.74 | 0 | Hydrophobic |
| C5 | CB | ALA- 293 | 3.96 | 0 | Hydrophobic |
| C20 | CB | ALA- 293 | 4.18 | 0 | Hydrophobic |
| C17 | CD | LYS- 295 | 4.19 | 0 | Hydrophobic |
| C20 | CB | LYS- 295 | 3.52 | 0 | Hydrophobic |
| C29 | CG | GLU- 310 | 3.91 | 0 | Hydrophobic |
| C17 | SD | MET- 314 | 3.58 | 0 | Hydrophobic |
| C15 | CE | MET- 314 | 4.12 | 0 | Hydrophobic |
| C28 | CG | MET- 314 | 4.16 | 0 | Hydrophobic |
| C29 | SD | MET- 314 | 3.8 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 317 | 4.33 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 322 | 4.4 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 323 | 4.25 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 323 | 4.27 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 336 | 3.56 | 0 | Hydrophobic |
| N13 | OG1 | THR- 338 | 3.09 | 132.38 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 338 | 4.09 | 0 | Hydrophobic |
| C14 | CG2 | THR- 338 | 3.56 | 0 | Hydrophobic |
| N3 | N | MET- 341 | 2.86 | 165.82 | H-Bond (Protein Donor) |
| N51 | O | VAL- 383 | 3.28 | 145.3 | H-Bond (Ligand Donor) |
| N51 | O | HIS- 384 | 3.43 | 123.38 | H-Bond (Ligand Donor) |
| C6 | CD2 | LEU- 393 | 3.89 | 0 | Hydrophobic |
| O29 | N | ASP- 404 | 2.72 | 177.61 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 404 | 3.7 | 0 | Hydrophobic |
