sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2009-07-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.680 | 7.160 | 7.400 | 0.340 | 7.400 | 3 |
| Name: | Tyrosine-protein kinase Lyn |
|---|---|
| ID: | LYN_HUMAN |
| AC: | P07948 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| X | 100 % |
| B-Factor: | 41.670 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.325 | 1245.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.57 | 47.43 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 52.28 % |
| 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 |
|---|---|---|
| -3.07463 | -22.4613 | -19.8306 |
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 |
| C5 | CD1 | LEU- 22 | 4.17 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 22 | 3.67 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 30 | 4.04 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 30 | 3.77 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 30 | 3.96 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 30 | 3.94 | 0 | Hydrophobic |
| C7 | CB | ALA- 42 | 4.26 | 0 | Hydrophobic |
| C15 | CD | LYS- 44 | 4.36 | 0 | Hydrophobic |
| N1 | O | GLU- 89 | 2.67 | 148.13 | H-Bond (Ligand Donor) |
| O5 | N | MET- 91 | 2.87 | 166.52 | H-Bond (Protein Donor) |
| N4 | O | ALA- 140 | 3.27 | 135.23 | H-Bond (Ligand Donor) |
| C22 | CD2 | LEU- 143 | 4.3 | 0 | Hydrophobic |
| C27 | CG | LEU- 143 | 3.64 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 143 | 3.22 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 143 | 3.7 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 143 | 3.9 | 0 | Hydrophobic |
| C27 | CB | ALA- 153 | 4.34 | 0 | Hydrophobic |
| C15 | CB | ASP- 154 | 4.33 | 0 | Hydrophobic |
