sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2013-05-04
| Name: | NTPase P4 |
|---|---|
| ID: | Q94M05_9VIRU |
| AC: | Q94M05 |
| Organism: | Pseudomonas phage phi12 |
| Reign: | Viruses |
| TaxID: | 161736 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 37 % |
| C | 63 % |
| B-Factor: | 39.264 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.116 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 32.86 | 67.14 |
| According to VolSite | |
| HET Code: | APC |
|---|---|
| Formula: | C11H14N5O12P3 |
| Molecular weight: | 501.176 g/mol |
| DrugBank ID: | DB02596 |
| Buried Surface Area: | 53.45 % |
| Polar Surface area: | 310.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 31.3929 | 53.391 | 26.8402 |
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 |
| O1G | NZ | LYS- 192 | 3.62 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 192 | 2.67 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 192 | 2.67 | 137.69 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 272 | 3.52 | 0 | Ionic (Protein Cationic) |
| C2' | CG | GLN- 278 | 4.29 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 288 | 3.63 | 0 | Aromatic Face/Face |
