sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 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: | 31.412 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.243 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 35.64 | 64.36 |
| According to VolSite | |
| HET Code: | BAB |
|---|---|
| Formula: | C17H18N8 |
| Molecular weight: | 334.378 g/mol |
| DrugBank ID: | DB01705 |
| Buried Surface Area: | 71.78 % |
| 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 |
|---|---|---|
| 10.4354 | 0.28972 | 24.8234 |
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 |
| C5 | CB | ASP- 68 | 4.15 | 0 | Hydrophobic |
| C3 | CB | ASP- 68 | 3.97 | 0 | Hydrophobic |
| C2 | CZ | TYR- 372 | 3.45 | 0 | Hydrophobic |
| C3' | CB | PHE- 373 | 3.6 | 0 | Hydrophobic |
| C9 | CB | ASP- 375 | 4.21 | 0 | Hydrophobic |
| N4 | OG | SER- 376 | 3.17 | 127.76 | H-Bond (Ligand Donor) |
| C5 | CB | SER- 376 | 4.28 | 0 | Hydrophobic |
| C9 | CB | GLU- 451 | 3.61 | 0 | Hydrophobic |
| C1' | CB | PHE- 455 | 3.72 | 0 | Hydrophobic |
| C2' | CB | THR- 709 | 3.81 | 0 | Hydrophobic |
| N3' | ZN | ZN- 1294 | 2.52 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 1294 | 3.38 | 135.83 | Pi/Cation |
