sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-12-17
| 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 | 23 % |
| B | 77 % |
| B-Factor: | 40.644 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.751 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.86 | 41.14 |
| According to VolSite | |
| HET Code: | LOC |
|---|---|
| Formula: | C22H25NO6 |
| Molecular weight: | 399.437 g/mol |
| DrugBank ID: | DB01394 |
| Buried Surface Area: | 74.97 % |
| 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 |
|---|---|---|
| 17.0192 | 65.9939 | 43.3901 |
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 | 3.87 | 0 | Hydrophobic |
| O5 | N | VAL- 181 | 3.05 | 144.16 | H-Bond (Protein Donor) |
| C18 | CG1 | VAL- 181 | 4.1 | 0 | Hydrophobic |
| C5 | CB | CYS- 241 | 4.38 | 0 | Hydrophobic |
| C6 | CB | CYS- 241 | 4.2 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 242 | 3.72 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 248 | 3.99 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 248 | 4.37 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 248 | 4.27 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 248 | 3.81 | 0 | Hydrophobic |
| C6 | CB | ALA- 250 | 4.37 | 0 | Hydrophobic |
| C7 | CB | ALA- 250 | 3.55 | 0 | Hydrophobic |
| C9 | CB | LYS- 254 | 3.7 | 0 | Hydrophobic |
| C9 | CB | LEU- 255 | 4.38 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 255 | 4.14 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 255 | 3.56 | 0 | Hydrophobic |
| C18 | SD | MET- 259 | 3.71 | 0 | Hydrophobic |
| C18 | CB | THR- 314 | 3.63 | 0 | Hydrophobic |
| C1 | CB | ALA- 316 | 4.39 | 0 | Hydrophobic |
| C2 | CB | ALA- 316 | 3.91 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 318 | 3.56 | 0 | Hydrophobic |
| C2 | CB | LYS- 352 | 4.35 | 0 | Hydrophobic |
| C18 | CG | LYS- 352 | 4.25 | 0 | Hydrophobic |
| C2 | CB | ALA- 354 | 4.2 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 378 | 3.83 | 0 | Hydrophobic |
| O3 | O | HOH- 728 | 3.46 | 179.98 | H-Bond (Protein Donor) |
