sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2009-02-22
| Name: | Polyribonucleotide nucleotidyltransferase |
|---|---|
| ID: | PNP_ECO24 |
| AC: | A7ZS61 |
| Organism: | Escherichia coli O139:H28 |
| Reign: | Bacteria |
| TaxID: | 331111 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 80 % |
| C | 20 % |
| B-Factor: | 31.956 |
|---|---|
| Number of residues: | 13 |
| Including | |
| Standard Amino Acids: | 10 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.197 | 1167.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.22 | 55.78 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 30.98 % |
| Polar Surface area: | 217.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -26.98 | -18.8071 | 18.0814 |
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 | SER- 76 | 4.16 | 0 | Hydrophobic |
| C2' | CB | SER- 76 | 4.17 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 77 | 4.47 | 0 | Hydrophobic |
| C1' | CD2 | PHE- 77 | 3.61 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 77 | 3.81 | 0 | Aromatic Face/Face |
| C1' | CZ | PHE- 78 | 4.32 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 366 | 2.98 | 161.06 | H-Bond (Ligand Donor) |
