sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-05-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.290 | 7.420 | 7.480 | 0.090 | 7.480 | 3 |
| Name: | Tyrosine-protein kinase Fyn |
|---|---|
| ID: | FYN_HUMAN |
| AC: | P06241 |
| 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: | 34.255 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.174 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 52.12 | 47.88 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 63.33 % |
| 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 |
|---|---|---|
| -16.6357 | 18.4042 | -12.7416 |
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 |
| C6 | CD1 | LEU- 17 | 4.05 | 0 | Hydrophobic |
| C20 | CB | LEU- 17 | 3.81 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 17 | 3.49 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 17 | 3.72 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 25 | 3.78 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 25 | 3.79 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 25 | 4.08 | 0 | Hydrophobic |
| C7 | CB | ALA- 37 | 4.02 | 0 | Hydrophobic |
| C14 | CD | LYS- 39 | 3.69 | 0 | Hydrophobic |
| N1 | O | GLU- 83 | 2.85 | 177.71 | H-Bond (Ligand Donor) |
| O5 | N | MET- 85 | 2.98 | 179.18 | H-Bond (Protein Donor) |
| C24 | CB | SER- 89 | 4.38 | 0 | Hydrophobic |
| N4 | O | ALA- 134 | 2.84 | 135.76 | H-Bond (Ligand Donor) |
| C24 | CD2 | LEU- 137 | 4.35 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 137 | 4.03 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 137 | 3.89 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 137 | 3.35 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 137 | 3.35 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 137 | 4.06 | 0 | Hydrophobic |
| C13 | CB | ALA- 147 | 4.34 | 0 | Hydrophobic |
| C27 | CB | ALA- 147 | 4.11 | 0 | Hydrophobic |
| C27 | CB | ASP- 148 | 4.44 | 0 | Hydrophobic |
| C15 | CB | ASP- 148 | 3.45 | 0 | Hydrophobic |
