sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2016-03-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.110 | 6.110 | 6.110 | 0.000 | 6.110 | 1 |
| Name: | Tubulin beta-2B chain |
|---|---|
| ID: | TBB2B_BOVIN |
| AC: | Q6B856 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 21 % |
| B | 79 % |
| B-Factor: | 39.959 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.070 | 1603.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.58 | 56.42 |
| According to VolSite | |
| HET Code: | LOC |
|---|---|
| Formula: | C22H25NO6 |
| Molecular weight: | 399.437 g/mol |
| DrugBank ID: | DB01394 |
| Buried Surface Area: | 76.67 % |
| Polar Surface area: | 83.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -2.79341 | 21.702 | -26.9137 |
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 |
| C13 | CB | SER- 178 | 4.15 | 0 | Hydrophobic |
| O5 | N | VAL- 181 | 3.13 | 154.23 | H-Bond (Protein Donor) |
| C18 | CG1 | VAL- 181 | 4.18 | 0 | Hydrophobic |
| C6 | CB | CYS- 241 | 3.98 | 0 | Hydrophobic |
| C5 | CB | CYS- 241 | 4.14 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 242 | 3.54 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 248 | 4.3 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 248 | 3.94 | 0 | Hydrophobic |
| C6 | CB | ALA- 250 | 4.33 | 0 | Hydrophobic |
| C7 | CB | ALA- 250 | 3.64 | 0 | Hydrophobic |
| C10 | CG | LYS- 254 | 3.92 | 0 | Hydrophobic |
| C9 | CB | LEU- 255 | 4.21 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 255 | 4.21 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 255 | 3.45 | 0 | Hydrophobic |
| C18 | SD | MET- 259 | 3.76 | 0 | Hydrophobic |
| C18 | CB | THR- 314 | 3.6 | 0 | Hydrophobic |
| C1 | CB | ALA- 316 | 4.01 | 0 | Hydrophobic |
| C2 | CB | ALA- 316 | 3.42 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 318 | 4.34 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 318 | 3.65 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 318 | 3.72 | 0 | Hydrophobic |
| C13 | CD | LYS- 352 | 4.23 | 0 | Hydrophobic |
| C2 | CB | LYS- 352 | 4.3 | 0 | Hydrophobic |
| C18 | CB | LYS- 352 | 4.46 | 0 | Hydrophobic |
| C2 | CB | ALA- 354 | 4.04 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 378 | 3.62 | 0 | Hydrophobic |
