sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2005-10-20
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 45.033 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.375 | 573.750 |
| % Hydrophobic | % Polar |
|---|---|
| 59.41 | 40.59 |
| According to VolSite | |
| HET Code: | 24A |
|---|---|
| Formula: | C20H26N6O5P2 |
| Molecular weight: | 492.405 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.11 % |
| Polar Surface area: | 206.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -6.86433 | 39.091 | 19.4531 |
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 |
| CR1 | CD1 | LEU- 273 | 3.93 | 0 | Hydrophobic |
| CR6 | CB | LEU- 273 | 4 | 0 | Hydrophobic |
| CS3 | CB | LEU- 273 | 4.33 | 0 | Hydrophobic |
| CR4 | CD2 | LEU- 273 | 3.9 | 0 | Hydrophobic |
| C0A | CG1 | VAL- 281 | 4.16 | 0 | Hydrophobic |
| CS3 | CG2 | VAL- 281 | 3.93 | 0 | Hydrophobic |
| C0A | CB | ALA- 293 | 3.83 | 0 | Hydrophobic |
| C0A | CG | LYS- 295 | 3.74 | 0 | Hydrophobic |
| C0A | CG2 | THR- 338 | 4.31 | 0 | Hydrophobic |
| N7A | N | MET- 341 | 2.96 | 162.51 | H-Bond (Protein Donor) |
| N6A | O | MET- 341 | 2.73 | 130.98 | H-Bond (Ligand Donor) |
| CS6 | CB | SER- 345 | 3.68 | 0 | Hydrophobic |
| C1A | CD1 | LEU- 393 | 3.43 | 0 | Hydrophobic |
| CS5 | CD2 | LEU- 393 | 3.69 | 0 | Hydrophobic |
| NS1 | O | HOH- 860 | 3.1 | 165.25 | H-Bond (Ligand Donor) |
