sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-05-06
| Name: | Nitric oxide reductase |
|---|---|
| ID: | B3Y963_GEOSE |
| AC: | B3Y963 |
| Organism: | Geobacillus stearothermophilus |
| Reign: | Bacteria |
| TaxID: | 1422 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 63.433 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.476 | 799.875 |
| % Hydrophobic | % Polar |
|---|---|
| 59.92 | 40.08 |
| According to VolSite | |
| HET Code: | HQO |
|---|---|
| Formula: | C16H21NO2 |
| Molecular weight: | 259.343 g/mol |
| DrugBank ID: | DB07918 |
| Buried Surface Area: | 54.85 % |
| Polar Surface area: | 45.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 36.3424 | 35.8438 | -3.47842 |
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 |
| C2 | CB | ALA- 324 | 3.94 | 0 | Hydrophobic |
| C14 | CB | ALA- 324 | 3.88 | 0 | Hydrophobic |
| C16 | CB | LEU- 325 | 3.93 | 0 | Hydrophobic |
| C9 | CB | ALA- 327 | 3.61 | 0 | Hydrophobic |
| C6 | CB | HIS- 328 | 4.09 | 0 | Hydrophobic |
| C13 | CB | HIS- 328 | 4.14 | 0 | Hydrophobic |
| C7 | CG2 | THR- 331 | 3.88 | 0 | Hydrophobic |
| C11 | CE1 | PHE- 336 | 4.4 | 0 | Hydrophobic |
| C13 | CZ | PHE- 336 | 3.5 | 0 | Hydrophobic |
| C12 | CE1 | PHE- 336 | 3.51 | 0 | Hydrophobic |
| C15 | CZ | PHE- 336 | 3.91 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 337 | 3.56 | 0 | Hydrophobic |
| C8 | CB | ARG- 742 | 3.98 | 0 | Hydrophobic |
| C6 | CB | ALA- 743 | 4.44 | 0 | Hydrophobic |
| C10 | CB | ALA- 743 | 3.85 | 0 | Hydrophobic |
| C9 | CB | ALA- 743 | 3.95 | 0 | Hydrophobic |
| C1 | CB | ASP- 746 | 4.09 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 746 | 2.85 | 154.78 | H-Bond (Ligand Donor) |
