sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2009-09-28
| Name: | Succinate dehydrogenase iron-sulfur subunit | Succinate dehydrogenase cytochrome b556 subunit |
|---|---|---|
| ID: | SDHB_ECOLI | DHSC_ECOLI |
| AC: | P07014 | P69054 |
| Organism: | Escherichia coli | |
| Reign: | Bacteria | |
| TaxID: | 83333 | |
| EC Number: | 1.3.5.1 | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| F | 40 % |
| G | 50 % |
| H | 10 % |
| B-Factor: | 46.761 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 18 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.754 | 253.125 |
| % Hydrophobic | % Polar |
|---|---|
| 73.33 | 26.67 |
| According to VolSite | |
| HET Code: | CBE |
|---|---|
| Formula: | C12H13NO2S |
| Molecular weight: | 235.302 g/mol |
| DrugBank ID: | DB04657 |
| Buried Surface Area: | 71.03 % |
| Polar Surface area: | 63.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 55.5371 | -53.2566 | -25.2381 |
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 |
| C14 | CD1 | LEU- 15 | 4.29 | 0 | Hydrophobic |
| C5 | CB | SER- 27 | 3.98 | 0 | Hydrophobic |
| S4 | CD1 | ILE- 28 | 3.75 | 0 | Hydrophobic |
| C12 | CB | ILE- 28 | 4.12 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 28 | 3.65 | 0 | Hydrophobic |
| S4 | CB | ARG- 31 | 4.03 | 0 | Hydrophobic |
| O9 | OH | TYR- 83 | 2.65 | 144.26 | H-Bond (Protein Donor) |
| C1 | CB | PRO- 160 | 4.35 | 0 | Hydrophobic |
| C16 | CB | PRO- 160 | 4.12 | 0 | Hydrophobic |
| C12 | CG | PRO- 160 | 3.52 | 0 | Hydrophobic |
| O9 | NE1 | TRP- 164 | 2.91 | 163.74 | H-Bond (Protein Donor) |
| C6 | CB | HIS- 207 | 3.68 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 209 | 4.41 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 209 | 4.14 | 0 | Hydrophobic |
