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: | 9.100 | 9.100 | 9.100 | 0.000 | 9.100 | 1 |
| 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: | 11.838 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.966 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.54 | 46.46 |
| According to VolSite | |
| HET Code: | PP2 |
|---|---|
| Formula: | C15H16ClN5 |
| Molecular weight: | 301.774 g/mol |
| DrugBank ID: | DB03023 |
| Buried Surface Area: | 62.47 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 23.5535 | 37.2515 | 84.2959 |
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 |
| C24 | CB | LEU- 251 | 3.65 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 259 | 4.33 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 259 | 4.18 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 259 | 3.99 | 0 | Hydrophobic |
| C6 | CB | ALA- 271 | 3.99 | 0 | Hydrophobic |
| C12 | CB | ALA- 271 | 3.74 | 0 | Hydrophobic |
| C13 | CB | LYS- 273 | 3.81 | 0 | Hydrophobic |
| C14 | CD | LYS- 273 | 3.76 | 0 | Hydrophobic |
| CL | CG | GLU- 288 | 4.44 | 0 | Hydrophobic |
| CL | SD | MET- 292 | 4.37 | 0 | Hydrophobic |
| CL | CG2 | ILE- 314 | 3.46 | 0 | Hydrophobic |
| C13 | CG2 | THR- 316 | 3.61 | 0 | Hydrophobic |
| N25 | O | GLU- 317 | 2.86 | 158.55 | H-Bond (Ligand Donor) |
| N4 | N | MET- 319 | 3.1 | 166.68 | H-Bond (Protein Donor) |
| C23 | CB | SER- 323 | 4.11 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 371 | 3.53 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 371 | 3.95 | 0 | Hydrophobic |
