sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-05-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.520 | 7.580 | 7.520 | 0.080 | 7.700 | 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: | 9.556 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.405 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 56.43 | 43.57 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 54.31 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 25.2726 | 39.4028 | 83.9281 |
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 |
| C25 | CB | LEU- 251 | 4.4 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 251 | 4.08 | 0 | Hydrophobic |
| C20 | CB | LEU- 251 | 3.78 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 251 | 3.93 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 251 | 3.78 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 259 | 4.2 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 259 | 4.05 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 259 | 3.75 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 259 | 3.92 | 0 | Hydrophobic |
| C7 | CB | ALA- 271 | 4.15 | 0 | Hydrophobic |
| C14 | CD | LYS- 273 | 3.95 | 0 | Hydrophobic |
| N1 | O | GLU- 317 | 2.92 | 178.27 | H-Bond (Ligand Donor) |
| O5 | N | MET- 319 | 2.76 | 171.2 | H-Bond (Protein Donor) |
| N4 | OG | SER- 323 | 2.86 | 150.72 | H-Bond (Ligand Donor) |
| C27 | CD1 | LEU- 371 | 3.37 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 371 | 3.39 | 0 | Hydrophobic |
| C15 | CB | ASP- 382 | 4.17 | 0 | Hydrophobic |
