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
2008-12-30
| Name: | Soluble cytochrome b562 |
|---|---|
| ID: | C562_ECOLX |
| AC: | P0ABE7 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 73 % |
| B | 27 % |
| B-Factor: | 39.193 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.076 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 23.61 | 76.39 |
| According to VolSite | |
| HET Code: | PXX |
|---|---|
| Formula: | C14H11N3O |
| Molecular weight: | 237.257 g/mol |
| DrugBank ID: | DB08440 |
| Buried Surface Area: | 55.99 % |
| Polar Surface area: | 54.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -19.0903 | 14.4133 | -12.0651 |
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 |
| NAL | O | PRO- 53 | 3.06 | 130.1 | H-Bond (Ligand Donor) |
| CAH | CB | PRO- 53 | 4.25 | 0 | Hydrophobic |
| CAI | CB | MET- 58 | 4.17 | 0 | Hydrophobic |
| CAG | CE | MET- 58 | 3.85 | 0 | Hydrophobic |
| CAA | CB | CYS- 59 | 3.48 | 0 | Hydrophobic |
| CAI | CB | ALA- 62 | 3.69 | 0 | Hydrophobic |
| CAD | CB | ASP- 73 | 4.38 | 0 | Hydrophobic |
