sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2015-11-25
| Name: | Tubulin beta chain |
|---|---|
| ID: | D0VWY9_SHEEP |
| AC: | D0VWY9 |
| Organism: | Ovis aries |
| Reign: | Eukaryota |
| TaxID: | 9940 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 22 % |
| B | 78 % |
| B-Factor: | 38.200 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.711 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 58.06 | 41.94 |
| According to VolSite | |
| HET Code: | LOC |
|---|---|
| Formula: | C22H25NO6 |
| Molecular weight: | 399.437 g/mol |
| DrugBank ID: | DB01394 |
| Buried Surface Area: | 77.51 % |
| 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 |
|---|---|---|
| -17.4133 | 9.89621 | -25.6222 |
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 | 3.99 | 0 | Hydrophobic |
| O5 | N | VAL- 181 | 2.94 | 154.36 | H-Bond (Protein Donor) |
| C18 | CG2 | VAL- 181 | 4.38 | 0 | Hydrophobic |
| C6 | CB | CYS- 241 | 3.97 | 0 | Hydrophobic |
| C5 | CB | CYS- 241 | 4.28 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 242 | 3.62 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 248 | 3.98 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 248 | 4.15 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 248 | 3.95 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 248 | 3.73 | 0 | Hydrophobic |
| C6 | CB | ALA- 250 | 4.26 | 0 | Hydrophobic |
| C7 | CB | ALA- 250 | 3.63 | 0 | Hydrophobic |
| C10 | CG | LYS- 254 | 3.9 | 0 | Hydrophobic |
| C9 | CB | LEU- 255 | 4.45 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 255 | 3.9 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 255 | 3.68 | 0 | Hydrophobic |
| C18 | SD | MET- 259 | 3.88 | 0 | Hydrophobic |
| C18 | CB | THR- 314 | 3.75 | 0 | Hydrophobic |
| C1 | CB | ALA- 316 | 4.37 | 0 | Hydrophobic |
| C2 | CB | ALA- 316 | 4.2 | 0 | Hydrophobic |
| C4 | CB | ALA- 316 | 4.26 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 318 | 3.46 | 0 | Hydrophobic |
| C13 | CD | LYS- 352 | 4.48 | 0 | Hydrophobic |
| C2 | CB | LYS- 352 | 4.31 | 0 | Hydrophobic |
| C18 | CB | LYS- 352 | 4.31 | 0 | Hydrophobic |
| C2 | CB | ALA- 354 | 3.9 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 378 | 3.65 | 0 | Hydrophobic |
