sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2015-01-29
| Name: | Ribonuclease J |
|---|---|
| ID: | H9CZL7_DEIRD |
| AC: | H9CZL7 |
| Organism: | Deinococcus radiodurans |
| Reign: | Bacteria |
| TaxID: | 1299 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.937 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 1.065 | 1525.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.58 | 56.42 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.76 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -0.998762 | 196.344 | 22.0158 |
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 |
| O3P | OG | SER- 154 | 3.44 | 173.26 | H-Bond (Protein Donor) |
| C4' | CG2 | THR- 211 | 4.19 | 0 | Hydrophobic |
| C2' | CG1 | ILE- 347 | 3.89 | 0 | Hydrophobic |
| O1P | OG | SER- 379 | 2.55 | 152.9 | H-Bond (Protein Donor) |
| O3P | N | GLY- 380 | 3.3 | 128.77 | H-Bond (Protein Donor) |
| O2P | O | HOH- 866 | 3.49 | 155.49 | H-Bond (Protein Donor) |
