sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-08-28
| Name: | 3-ketosteroid dehydrogenase |
|---|---|
| ID: | Q9RA02_RHOER |
| AC: | Q9RA02 |
| Organism: | Rhodococcus erythropolis |
| Reign: | Bacteria |
| TaxID: | 1833 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 92 % |
| F | 8 % |
| B-Factor: | 33.129 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.123 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.85 | 47.15 |
| According to VolSite | |
| HET Code: | ANB |
|---|---|
| Formula: | C19H24O2 |
| Molecular weight: | 284.393 g/mol |
| DrugBank ID: | DB07373 |
| Buried Surface Area: | 64.11 % |
| Polar Surface area: | 34.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -112.14 | 18.5296 | 39.385 |
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 |
| C6 | CB | SER- 52 | 3.77 | 0 | Hydrophobic |
| C19 | CZ | PHE- 116 | 3.88 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 116 | 3.58 | 0 | Hydrophobic |
| C11 | CE2 | PHE- 294 | 3.92 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 294 | 4.17 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 296 | 4.07 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 296 | 4.01 | 0 | Hydrophobic |
| C19 | CE1 | TYR- 318 | 3.79 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 352 | 4.39 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 354 | 3.76 | 0 | Hydrophobic |
| O1 | OH | TYR- 487 | 2.62 | 145.08 | H-Bond (Protein Donor) |
| C6 | CB | PRO- 490 | 3.89 | 0 | Hydrophobic |
| O1 | N | GLY- 491 | 2.95 | 155.65 | H-Bond (Protein Donor) |
| C11 | C6 | FAD- 551 | 4.18 | 0 | Hydrophobic |
