sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2012-01-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.750 | 8.050 | 7.750 | 0.400 | 8.750 | 14 |
| Name: | Aurora kinase B |
|---|---|
| ID: | AURKB_HUMAN |
| AC: | Q96GD4 |
| 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: | 64.554 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.145 | 621.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.33 | 39.67 |
| According to VolSite | |
| HET Code: | VX6 |
|---|---|
| Formula: | C23H29N8OS |
| Molecular weight: | 465.594 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.06 % |
| Polar Surface area: | 128.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 20.8333 | -22.1292 | -10.3866 |
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 |
| C9 | CD2 | LEU- 83 | 3.89 | 0 | Hydrophobic |
| S23 | CB | LEU- 83 | 4.13 | 0 | Hydrophobic |
| C29 | CB | LEU- 83 | 4.23 | 0 | Hydrophobic |
| S23 | CD1 | PHE- 88 | 4.15 | 0 | Hydrophobic |
| C26 | CB | PHE- 88 | 4.44 | 0 | Hydrophobic |
| C28 | CB | PHE- 88 | 3.21 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 91 | 3.82 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 91 | 4.13 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 91 | 4.38 | 0 | Hydrophobic |
| C21 | CB | ALA- 104 | 3.83 | 0 | Hydrophobic |
| C35 | CD | LYS- 106 | 3.64 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 138 | 4.22 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 154 | 4.39 | 0 | Hydrophobic |
| C34 | CD1 | LEU- 154 | 3.92 | 0 | Hydrophobic |
| N19 | O | GLU- 155 | 2.88 | 141.79 | H-Bond (Ligand Donor) |
| N14 | O | ALA- 157 | 3.22 | 141.05 | H-Bond (Ligand Donor) |
| N20 | N | ALA- 157 | 2.89 | 166.52 | H-Bond (Protein Donor) |
| C25 | CB | GLU- 161 | 4.44 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 207 | 3.48 | 0 | Hydrophobic |
| C34 | CB | ALA- 217 | 4.26 | 0 | Hydrophobic |
| C34 | CD1 | PHE- 219 | 4.08 | 0 | Hydrophobic |
| C35 | CB | PHE- 219 | 3.99 | 0 | Hydrophobic |
