sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.180 Å
X-ray
2012-06-23
| Name: | Sialidase B |
|---|---|
| ID: | NANB_STRPN |
| AC: | Q54727 |
| Organism: | Streptococcus pneumoniae serotype 4 |
| Reign: | Bacteria |
| TaxID: | 170187 |
| EC Number: | 3.2.1.18 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.212 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.725 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.43 | 60.57 |
| According to VolSite | |
| HET Code: | 0V8 |
|---|---|
| Formula: | C9H12BrNO3S |
| Molecular weight: | 294.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.61 % |
| Polar Surface area: | 82.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 5.03227 | -6.39013 | 36.4385 |
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 |
| OAC | NH1 | ARG- 245 | 2.97 | 151.65 | H-Bond (Protein Donor) |
| OAC | NH2 | ARG- 245 | 3.11 | 143.48 | H-Bond (Protein Donor) |
| OAC | CZ | ARG- 245 | 3.48 | 0 | Ionic (Protein Cationic) |
| CAH | CB | ASP- 270 | 4.35 | 0 | Hydrophobic |
| BR | CB | ASP- 270 | 4.11 | 0 | Hydrophobic |
| NAL | OD1 | ASP- 270 | 2.9 | 149.01 | H-Bond (Ligand Donor) |
| NAL | OD1 | ASP- 270 | 2.9 | 0 | Ionic (Ligand Cationic) |
| BR | CB | SER- 271 | 4.1 | 0 | Hydrophobic |
| CAF | CG2 | ILE- 326 | 3.62 | 0 | Hydrophobic |
| CAM | CD1 | ILE- 326 | 3.95 | 0 | Hydrophobic |
| CAF | CE | MET- 346 | 3.37 | 0 | Hydrophobic |
| OAB | NH1 | ARG- 557 | 2.97 | 154.24 | H-Bond (Protein Donor) |
| OAB | NH2 | ARG- 557 | 3.17 | 142.25 | H-Bond (Protein Donor) |
| OAB | CZ | ARG- 557 | 3.51 | 0 | Ionic (Protein Cationic) |
| OAB | CZ | ARG- 619 | 3.73 | 0 | Ionic (Protein Cationic) |
| OAC | CZ | ARG- 619 | 3.6 | 0 | Ionic (Protein Cationic) |
| OAB | NH2 | ARG- 619 | 2.79 | 169.79 | H-Bond (Protein Donor) |
| OAC | NH1 | ARG- 619 | 2.8 | 170.35 | H-Bond (Protein Donor) |
| CAJ | CZ | TYR- 653 | 3.92 | 0 | Hydrophobic |
