sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2014-10-24
| Name: | DUTPase |
|---|---|
| ID: | Q8SDV3_BPPHA |
| AC: | Q8SDV3 |
| Organism: | Staphylococcus phage phi11 |
| Reign: | Viruses |
| TaxID: | 12360 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 39 % |
| F | 61 % |
| B-Factor: | 36.490 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.179 | 415.125 |
| % Hydrophobic | % Polar |
|---|---|
| 32.52 | 67.48 |
| According to VolSite | |
| HET Code: | DUP |
|---|---|
| Formula: | C9H12N3O13P3 |
| Molecular weight: | 463.125 g/mol |
| DrugBank ID: | DB01965 |
| Buried Surface Area: | 55.92 % |
| Polar Surface area: | 282.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 13 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -10.3214 | -4.046 | -64.7344 |
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 |
| O1B | NH2 | ARG- 64 | 3.44 | 130.46 | H-Bond (Protein Donor) |
| O1B | NE | ARG- 64 | 2.93 | 152.41 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 64 | 3.6 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 64 | 3.8 | 0 | Ionic (Protein Cationic) |
| O2A | N | SER- 65 | 3.23 | 150.01 | H-Bond (Protein Donor) |
| O2B | N | GLY- 66 | 2.99 | 148.57 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 80 | 3.48 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 81 | 2.75 | 172.2 | H-Bond (Ligand Donor) |
| O3' | N | ASP- 81 | 3.15 | 168.91 | H-Bond (Protein Donor) |
| C1' | CE2 | TYR- 84 | 3.73 | 0 | Hydrophobic |
| C2' | CD2 | TYR- 84 | 3.81 | 0 | Hydrophobic |
| C3' | CG | TYR- 84 | 4.08 | 0 | Hydrophobic |
| C4' | CD1 | TYR- 84 | 3.74 | 0 | Hydrophobic |
| N3 | O | GLY- 89 | 2.8 | 173.79 | H-Bond (Ligand Donor) |
| O2 | N | GLY- 89 | 3.06 | 172.08 | H-Bond (Protein Donor) |
| O2A | NE2 | GLN- 136 | 3.15 | 128.95 | H-Bond (Protein Donor) |
| O1A | MG | MG- 201 | 2.52 | 0 | Metal Acceptor |
| O1B | MG | MG- 201 | 2.39 | 0 | Metal Acceptor |
| O3G | MG | MG- 201 | 2.58 | 0 | Metal Acceptor |
| O4 | O | HOH- 307 | 3 | 133.36 | H-Bond (Protein Donor) |
