sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
1999-03-11
| Name: | Seminal ribonuclease |
|---|---|
| ID: | RNS_BOVIN |
| AC: | P00669 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 3.1.27.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 82 % |
| B | 18 % |
| B-Factor: | 19.012 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.138 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 20.28 | 79.72 |
| According to VolSite | |
| HET Code: | U2G |
|---|---|
| Formula: | C19H23N7O13P |
| Molecular weight: | 588.399 g/mol |
| DrugBank ID: | DB04514 |
| Buried Surface Area: | 27.36 % |
| Polar Surface area: | 302.48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 7 |
| Rings: | 5 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -1.95547 | 32.1738 | 68.1577 |
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 |
| C2B | CB | ASN- 24 | 4.17 | 0 | Hydrophobic |
| C1B | CB | ASN- 27 | 4.03 | 0 | Hydrophobic |
| C1B | CD2 | LEU- 28 | 4.36 | 0 | Hydrophobic |
| O6G | NE | ARG- 33 | 3.07 | 140.54 | H-Bond (Protein Donor) |
| N7G | NH2 | ARG- 33 | 2.89 | 173.68 | H-Bond (Protein Donor) |
