sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2008-03-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.920 | 6.920 | 6.920 | 0.000 | 6.920 | 2 |
| Name: | Serine/threonine-protein kinase 24 |
|---|---|
| ID: | STK24_HUMAN |
| AC: | Q9Y6E0 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 53.729 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 52.31 | 47.69 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 64.82 % |
| 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 |
|---|---|---|
| -13.4153 | -1.551 | 11.477 |
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 | ILE- 15 | 3.85 | 0 | Hydrophobic |
| C1 | CB | ILE- 15 | 4.14 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 15 | 3.59 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 23 | 3.7 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 23 | 3.65 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 23 | 4.03 | 0 | Hydrophobic |
| C7 | CB | ALA- 36 | 4.18 | 0 | Hydrophobic |
| C12 | CE | MET- 84 | 4.13 | 0 | Hydrophobic |
| C14 | CE | MET- 84 | 3.63 | 0 | Hydrophobic |
| C13 | SD | MET- 84 | 4.17 | 0 | Hydrophobic |
| N1 | O | GLU- 85 | 2.66 | 170.7 | H-Bond (Ligand Donor) |
| O5 | N | LEU- 87 | 2.61 | 144.83 | H-Bond (Protein Donor) |
| C27 | CD2 | LEU- 136 | 4.31 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 136 | 3.55 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 136 | 3.27 | 0 | Hydrophobic |
| C13 | CB | ALA- 146 | 4.47 | 0 | Hydrophobic |
| C15 | CB | ASP- 147 | 3.7 | 0 | Hydrophobic |
