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
2013-09-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 3 |
| 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: | 38.785 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.011 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 59.03 | 40.97 |
| According to VolSite | |
| HET Code: | DB8 |
|---|---|
| Formula: | C26H30Cl2N5O3 |
| Molecular weight: | 531.454 g/mol |
| DrugBank ID: | DB06616 |
| Buried Surface Area: | 53.73 % |
| Polar Surface area: | 84.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 12.0895 | -37.176 | -6.81842 |
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 |
| CAA | CB | LEU- 273 | 3.92 | 0 | Hydrophobic |
| CAM | CD2 | LEU- 273 | 4.43 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 273 | 4.15 | 0 | Hydrophobic |
| CBD | CD1 | LEU- 273 | 3.45 | 0 | Hydrophobic |
| CBC | CD1 | LEU- 273 | 3.6 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 281 | 4.41 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 281 | 4.38 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 281 | 3.91 | 0 | Hydrophobic |
| CAJ | CB | ALA- 293 | 4.42 | 0 | Hydrophobic |
| CBG | CB | ALA- 293 | 4.42 | 0 | Hydrophobic |
| C01 | CB | ALA- 293 | 3.87 | 0 | Hydrophobic |
| CBA | CB | ALA- 293 | 4.07 | 0 | Hydrophobic |
| CAI | CD | LYS- 295 | 4.38 | 0 | Hydrophobic |
| C01 | CB | LYS- 295 | 3.73 | 0 | Hydrophobic |
| CL1 | CD | LYS- 295 | 3.75 | 0 | Hydrophobic |
| CAX | CB | LYS- 295 | 3.76 | 0 | Hydrophobic |
| CL1 | CG | GLU- 310 | 4.19 | 0 | Hydrophobic |
| CL1 | CE | MET- 314 | 3.36 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 336 | 3.7 | 0 | Hydrophobic |
| CAX | CG2 | THR- 338 | 3.93 | 0 | Hydrophobic |
| C01 | CG2 | THR- 338 | 3.73 | 0 | Hydrophobic |
| CAY | CG2 | THR- 338 | 4.37 | 0 | Hydrophobic |
| CAN | CZ | TYR- 340 | 3.85 | 0 | Hydrophobic |
| NAT | N | MET- 341 | 2.82 | 165.45 | H-Bond (Protein Donor) |
| CBE | CD1 | LEU- 393 | 3.42 | 0 | Hydrophobic |
| CL2 | CB | ALA- 403 | 4.37 | 0 | Hydrophobic |
| CL2 | CB | ASP- 404 | 3.97 | 0 | Hydrophobic |
