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
2007-10-19
| 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: | 22.639 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.349 | 1350.000 |
| % Hydrophobic | % Polar |
|---|---|
| 53.00 | 47.00 |
| According to VolSite | |
| HET Code: | 9NH |
|---|---|
| Formula: | C31H30F4N7O3 |
| Molecular weight: | 624.609 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.94 % |
| Polar Surface area: | 125.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 14.5309 | -4.21982 | 13.4448 |
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 |
| C31 | CD1 | LEU- 251 | 4.45 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 251 | 4.38 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 259 | 3.29 | 0 | Hydrophobic |
| C16 | CB | ALA- 271 | 3.92 | 0 | Hydrophobic |
| C18 | CB | ALA- 271 | 3.43 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 273 | 3.96 | 155.3 | Pi/Cation |
| C16 | CB | LYS- 273 | 3.88 | 0 | Hydrophobic |
| N3 | OE2 | GLU- 288 | 2.68 | 144.75 | H-Bond (Ligand Donor) |
| C7 | CG | GLU- 288 | 3.35 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 291 | 4.33 | 0 | Hydrophobic |
| C23 | SD | MET- 292 | 3.96 | 0 | Hydrophobic |
| F3 | CG | MET- 292 | 3.93 | 0 | Hydrophobic |
| C11 | CG | MET- 292 | 3.72 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 295 | 3.99 | 0 | Hydrophobic |
| F3 | CB | LEU- 295 | 4.39 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 300 | 3.26 | 0 | Hydrophobic |
| F4 | CB | VAL- 301 | 3.4 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 301 | 4.09 | 0 | Hydrophobic |
| C22 | CG2 | ILE- 314 | 3.5 | 0 | Hydrophobic |
| C15 | CG2 | THR- 316 | 3.7 | 0 | Hydrophobic |
| C22 | CG2 | THR- 316 | 3.64 | 0 | Hydrophobic |
| C5 | CE1 | TYR- 318 | 3.37 | 0 | Hydrophobic |
| N1 | N | MET- 319 | 3.04 | 168.65 | H-Bond (Protein Donor) |
| N7 | O | MET- 319 | 2.92 | 156.15 | H-Bond (Ligand Donor) |
| C18 | CD1 | LEU- 371 | 3.52 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 371 | 4.4 | 0 | Hydrophobic |
| O2 | N | ASP- 382 | 2.84 | 170.15 | H-Bond (Protein Donor) |
| F1 | CZ | PHE- 383 | 3.22 | 0 | Hydrophobic |
| C8 | CB | PHE- 383 | 3.74 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 383 | 4 | 0 | Hydrophobic |
