sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.890 Å
X-ray
2010-12-10
| Name: | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS |
|---|---|
| ID: | YOSS_BACSU |
| AC: | O34919 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | 3.6.1.23 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 12 % |
| D | 67 % |
| F | 21 % |
| B-Factor: | 20.389 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.014 | 1306.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.31 | 59.69 |
| According to VolSite | |
| HET Code: | DUD |
|---|---|
| Formula: | C9H11N2O11P2 |
| Molecular weight: | 385.138 g/mol |
| DrugBank ID: | DB03413 |
| Buried Surface Area: | 48.95 % |
| Polar Surface area: | 220.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -6.61775 | 34.9391 | -45.8864 |
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 |
| O3A | OG | SER- 62 | 3.05 | 121.21 | H-Bond (Protein Donor) |
| O1B | OG | SER- 62 | 3.38 | 136.85 | H-Bond (Protein Donor) |
| O4 | ND2 | ASN- 74 | 2.95 | 158.19 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 79 | 3.81 | 0 | Hydrophobic |
| C1' | CZ | TYR- 83 | 3.85 | 0 | Hydrophobic |
| C2' | CD2 | TYR- 83 | 3.79 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 83 | 3.94 | 0 | Hydrophobic |
| N3 | O | PHE- 91 | 2.85 | 166.61 | H-Bond (Ligand Donor) |
| O2 | N | PHE- 91 | 2.82 | 151.45 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 101 | 2.63 | 164.67 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 101 | 2.63 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 103 | 3.01 | 135.44 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 103 | 3.13 | 141.54 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 103 | 3.01 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 103 | 3.13 | 0 | Ionic (Protein Cationic) |
