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
2008-09-20
| 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: | 51.408 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.707 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.94 | 36.06 |
| According to VolSite | |
| HET Code: | PD5 |
|---|---|
| Formula: | C22H20F3N7O |
| Molecular weight: | 455.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.15 % |
| Polar Surface area: | 110.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 1.70976 | 4.84112 | 7.89391 |
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 | 4.33 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 281 | 4.5 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 281 | 3.52 | 0 | Hydrophobic |
| C5 | CB | ALA- 293 | 4.13 | 0 | Hydrophobic |
| CAM | CD | LYS- 295 | 3.75 | 0 | Hydrophobic |
| NAU | OE2 | GLU- 310 | 3.47 | 164.46 | H-Bond (Ligand Donor) |
| CAJ | CG | GLU- 310 | 3.42 | 0 | Hydrophobic |
| CAH | CG2 | VAL- 313 | 3.46 | 0 | Hydrophobic |
| CAP | SD | MET- 314 | 3.51 | 0 | Hydrophobic |
| CAK | CG | MET- 314 | 3.65 | 0 | Hydrophobic |
| CBA | CG | MET- 314 | 3.68 | 0 | Hydrophobic |
| FAF | CD1 | LEU- 317 | 3.62 | 0 | Hydrophobic |
| FAG | CD1 | LEU- 317 | 4.33 | 0 | Hydrophobic |
| FAF | CD1 | LEU- 322 | 4 | 0 | Hydrophobic |
| FAE | CB | LEU- 322 | 4.18 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 323 | 4.18 | 0 | Hydrophobic |
| NAC | O | GLU- 339 | 3.07 | 158.42 | H-Bond (Ligand Donor) |
| N1 | N | MET- 341 | 3 | 164.87 | H-Bond (Protein Donor) |
| C5 | CD1 | LEU- 393 | 3.53 | 0 | Hydrophobic |
| CAB | CD2 | LEU- 393 | 4.12 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 393 | 3.25 | 0 | Hydrophobic |
| FAG | CG1 | VAL- 402 | 4.45 | 0 | Hydrophobic |
| CAL | CB | ALA- 403 | 3.75 | 0 | Hydrophobic |
| OAD | N | ASP- 404 | 3.49 | 163.33 | H-Bond (Protein Donor) |
| CAK | CB | ALA- 408 | 4.03 | 0 | Hydrophobic |
