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
2007-01-05
| 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: | 23.401 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.277 | 685.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.13 | 41.87 |
| According to VolSite | |
| HET Code: | 1N8 |
|---|---|
| Formula: | C30H32F3N6O2 |
| Molecular weight: | 565.609 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.84 % |
| Polar Surface area: | 100.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 5.77917 | 28.6202 | 56.7632 |
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 |
| C10 | CD1 | LEU- 251 | 4.46 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 259 | 3.87 | 0 | Hydrophobic |
| C25 | CB | ALA- 271 | 3.86 | 0 | Hydrophobic |
| C3 | CB | ALA- 271 | 3.41 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 273 | 3.77 | 156.46 | Pi/Cation |
| C25 | CB | LYS- 273 | 3.93 | 0 | Hydrophobic |
| N3 | OE2 | GLU- 288 | 3.16 | 172.77 | H-Bond (Ligand Donor) |
| C18 | CD2 | LEU- 291 | 4.01 | 0 | Hydrophobic |
| C11 | CE | MET- 292 | 4.17 | 0 | Hydrophobic |
| F1 | CG | MET- 292 | 3.96 | 0 | Hydrophobic |
| C23 | SD | MET- 292 | 3.6 | 0 | Hydrophobic |
| C16 | CG | MET- 292 | 3.81 | 0 | Hydrophobic |
| F3 | CD1 | LEU- 295 | 3.42 | 0 | Hydrophobic |
| F2 | CD2 | LEU- 300 | 3.51 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 301 | 4.15 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 301 | 4.17 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 314 | 4.01 | 0 | Hydrophobic |
| C25 | CG2 | THR- 316 | 3.84 | 0 | Hydrophobic |
| C22 | CG2 | THR- 316 | 3.43 | 0 | Hydrophobic |
| C1 | CE1 | TYR- 318 | 3.59 | 0 | Hydrophobic |
| N1 | N | MET- 319 | 2.79 | 176.7 | H-Bond (Protein Donor) |
| N2 | O | MET- 319 | 2.72 | 154.51 | H-Bond (Ligand Donor) |
| C3 | CD1 | LEU- 371 | 3.85 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 380 | 4.49 | 0 | Hydrophobic |
| C19 | CB | ASP- 382 | 3.9 | 0 | Hydrophobic |
| O1 | N | ASP- 382 | 2.95 | 161.76 | H-Bond (Protein Donor) |
| N4 | O | ASP- 382 | 3.17 | 134.44 | H-Bond (Ligand Donor) |
| N6 | OD2 | ASP- 382 | 3.62 | 0 | Ionic (Ligand Cationic) |
