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
2000-11-22
| Name: | Botulinum neurotoxin type B |
|---|---|
| ID: | BXB_CLOBO |
| AC: | P10844 |
| Organism: | Clostridium botulinum |
| Reign: | Bacteria |
| TaxID: | 1491 |
| EC Number: | 3.4.24.69 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.709 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.780 | 1366.875 |
| % Hydrophobic | % Polar |
|---|---|
| 25.93 | 74.07 |
| According to VolSite | |
| HET Code: | BAB |
|---|---|
| Formula: | C17H18N8 |
| Molecular weight: | 334.378 g/mol |
| DrugBank ID: | DB01705 |
| Buried Surface Area: | 73.14 % |
| Polar Surface area: | 160.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 10.7484 | 0.33008 | 24.7997 |
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 |
| C3 | CB | ASP- 68 | 4.04 | 0 | Hydrophobic |
| N2 | O | TYR- 372 | 3.49 | 148.75 | H-Bond (Ligand Donor) |
| C3' | CB | PHE- 373 | 3.79 | 0 | Hydrophobic |
| N4 | O | SER- 374 | 2.89 | 124.53 | H-Bond (Ligand Donor) |
| C9 | CB | ASP- 375 | 4.17 | 0 | Hydrophobic |
| C5 | CB | SER- 376 | 4.46 | 0 | Hydrophobic |
| C9 | CB | GLU- 451 | 3.69 | 0 | Hydrophobic |
| C1' | CB | PHE- 455 | 3.6 | 0 | Hydrophobic |
| C2' | CB | THR- 709 | 3.7 | 0 | Hydrophobic |
| C2' | CB | TYR- 712 | 4.36 | 0 | Hydrophobic |
| C3' | CD2 | TYR- 712 | 3.45 | 0 | Hydrophobic |
| N1' | OG1 | THR- 713 | 2.54 | 168.14 | H-Bond (Ligand Donor) |
| N3 | ZN | ZN- 1294 | 2.55 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 1294 | 3.96 | 138.92 | Pi/Cation |
