sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
1999-05-25
| 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: | 18.764 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.164 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 54.70 | 45.30 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 61.2 % |
| 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 |
|---|---|---|
| 21.8159 | 14.4223 | 14.6144 |
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 |
| C4 | CD1 | LEU- 251 | 4.15 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 251 | 3.89 | 0 | Hydrophobic |
| C20 | CB | LEU- 251 | 3.81 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 259 | 4.1 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 259 | 4.06 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 259 | 3.77 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 259 | 3.91 | 0 | Hydrophobic |
| C10 | CB | ALA- 271 | 4.1 | 0 | Hydrophobic |
| C14 | CD | LYS- 273 | 4.17 | 0 | Hydrophobic |
| N1 | O | GLU- 317 | 2.85 | 161.72 | H-Bond (Ligand Donor) |
| O5 | N | MET- 319 | 2.85 | 164.4 | H-Bond (Protein Donor) |
| C24 | CB | SER- 323 | 4.29 | 0 | Hydrophobic |
| N4 | OG | SER- 323 | 2.72 | 121.52 | H-Bond (Ligand Donor) |
| N4 | O | ALA- 368 | 3.21 | 144.45 | H-Bond (Ligand Donor) |
| C27 | CD2 | LEU- 371 | 4.05 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 371 | 3.5 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 371 | 3.98 | 0 | Hydrophobic |
| C27 | CB | ALA- 381 | 4.4 | 0 | Hydrophobic |
| C15 | CB | ASP- 382 | 3.79 | 0 | Hydrophobic |
