sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2007-04-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.210 | 7.340 | 7.400 | 0.090 | 7.400 | 3 |
| Name: | Tyrosine-protein kinase Lck |
|---|---|
| ID: | LCK_HUMAN |
| AC: | P06239 |
| 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: | 49.908 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.072 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.41 | 44.59 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 61.07 % |
| 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 |
|---|---|---|
| 25.3141 | 17.4839 | 12.409 |
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 | CG1 | VAL- 259 | 4.25 | 0 | Hydrophobic |
| C12 | CB | ALA- 271 | 4.36 | 0 | Hydrophobic |
| C20 | CB | ALA- 271 | 4.06 | 0 | Hydrophobic |
| C6 | CB | ALA- 271 | 3.82 | 0 | Hydrophobic |
| C17 | CD | LYS- 273 | 4.24 | 0 | Hydrophobic |
| C18 | CB | LYS- 273 | 3.6 | 0 | Hydrophobic |
| C25 | CG | GLU- 288 | 3.9 | 0 | Hydrophobic |
| C17 | SD | MET- 292 | 3.66 | 0 | Hydrophobic |
| C15 | CE | MET- 292 | 4.09 | 0 | Hydrophobic |
| C23 | SD | MET- 292 | 4.32 | 0 | Hydrophobic |
| C25 | CG | MET- 292 | 4.14 | 0 | Hydrophobic |
| C28 | CD1 | LEU- 300 | 4.15 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 301 | 4.47 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 301 | 3.89 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 314 | 3.62 | 0 | Hydrophobic |
| N13 | OG1 | THR- 316 | 2.73 | 133.05 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 316 | 4.4 | 0 | Hydrophobic |
| C14 | CG2 | THR- 316 | 3.52 | 0 | Hydrophobic |
| C1 | CB | TYR- 318 | 4.31 | 0 | Hydrophobic |
| C1 | CB | MET- 319 | 3.81 | 0 | Hydrophobic |
| N51 | O | ILE- 361 | 2.73 | 173.93 | H-Bond (Ligand Donor) |
| C1 | CD2 | LEU- 371 | 4.35 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 371 | 3.98 | 0 | Hydrophobic |
| O29 | N | ASP- 382 | 2.95 | 159.78 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 382 | 3.78 | 0 | Hydrophobic |
