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
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.960 | 7.960 | 7.960 | 0.000 | 7.960 | 1 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 42.475 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.254 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.18 | 43.82 |
| According to VolSite | |
| HET Code: | 1N1 |
|---|---|
| Formula: | C22H27ClN7O2S |
| Molecular weight: | 489.013 g/mol |
| DrugBank ID: | DB01254 |
| Buried Surface Area: | 58.42 % |
| Polar Surface area: | 135.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 2.95964 | -68.9782 | 30.7146 |
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 |
| C12 | CD1 | LEU- 273 | 4.03 | 0 | Hydrophobic |
| C15 | CB | LEU- 273 | 4.06 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 273 | 4.23 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 273 | 4.31 | 0 | Hydrophobic |
| S | CD1 | LEU- 273 | 4.49 | 0 | Hydrophobic |
| S | CG1 | VAL- 281 | 3.72 | 0 | Hydrophobic |
| C10 | CB | ALA- 293 | 3.95 | 0 | Hydrophobic |
| S | CB | ALA- 293 | 4.1 | 0 | Hydrophobic |
| C8 | CD | LYS- 295 | 3.5 | 0 | Hydrophobic |
| C10 | CB | LYS- 295 | 3.51 | 0 | Hydrophobic |
| C6 | SD | MET- 314 | 3.61 | 0 | Hydrophobic |
| CL | CG1 | VAL- 323 | 3.55 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 336 | 3.78 | 0 | Hydrophobic |
| N2 | OG1 | THR- 338 | 2.92 | 138.12 | H-Bond (Ligand Donor) |
| C5 | CG2 | THR- 338 | 3.9 | 0 | Hydrophobic |
| C9 | CG2 | THR- 338 | 3.4 | 0 | Hydrophobic |
| C19 | CZ | TYR- 340 | 4.27 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 340 | 3.5 | 0 | Hydrophobic |
| N | O | MET- 341 | 2.79 | 143.39 | H-Bond (Ligand Donor) |
| N1 | N | MET- 341 | 3.03 | 173.13 | H-Bond (Protein Donor) |
| O1 | O | SER- 342 | 3.34 | 140.67 | H-Bond (Ligand Donor) |
| S | CD1 | LEU- 393 | 3.88 | 0 | Hydrophobic |
| CL | CD1 | LEU- 393 | 4.41 | 0 | Hydrophobic |
| CL | CB | ALA- 403 | 3.86 | 0 | Hydrophobic |
