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
2012-01-31
| Name: | Ribosomal oxygenase 1 |
|---|---|
| ID: | NO66_HUMAN |
| AC: | Q9H6W3 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 48.804 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.030 | 1255.500 |
| % Hydrophobic | % Polar |
|---|---|
| 30.65 | 69.35 |
| According to VolSite | |
| HET Code: | PD2 |
|---|---|
| Formula: | C7H3NO4 |
| Molecular weight: | 165.103 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.45 % |
| Polar Surface area: | 93.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -24.9385 | -51.344 | -8.01417 |
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 | PHE- 337 | 3.77 | 0 | Hydrophobic |
| O42 | NZ | LYS- 355 | 2.66 | 176.16 | H-Bond (Protein Donor) |
| O42 | NZ | LYS- 355 | 2.66 | 0 | Ionic (Protein Cationic) |
| O41 | NZ | LYS- 355 | 3.86 | 0 | Ionic (Protein Cationic) |
| O21 | NE2 | HIS- 417 | 2.9 | 167.95 | H-Bond (Protein Donor) |
