sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.100 Å
X-ray
2003-05-21
| Name: | Steroid Delta-isomerase |
|---|---|
| ID: | SDIS_PSEPU |
| AC: | P07445 |
| Organism: | Pseudomonas putida |
| Reign: | Bacteria |
| TaxID: | 303 |
| EC Number: | 5.3.3.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 11.441 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.830 | 381.375 |
| % Hydrophobic | % Polar |
|---|---|
| 61.95 | 38.05 |
| According to VolSite | |
| HET Code: | EQU |
|---|---|
| Formula: | C18H18O2 |
| Molecular weight: | 266.334 g/mol |
| DrugBank ID: | DB03515 |
| Buried Surface Area: | 60.27 % |
| Polar Surface area: | 37.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 13.2561 | -46.3178 | -14.7716 |
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 |
| O1 | OH | TYR- 216 | 2.55 | 161.52 | H-Bond (Protein Donor) |
| C6 | CG1 | VAL- 220 | 4.03 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 261 | 4.04 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 266 | 4.06 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 288 | 4.22 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 288 | 4.14 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 288 | 3.83 | 0 | Hydrophobic |
| C25 | SD | MET- 290 | 3.78 | 0 | Hydrophobic |
| C16 | SD | MET- 290 | 4.31 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 299 | 3.59 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 301 | 4.35 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 301 | 4.08 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 303 | 2.56 | 124.81 | H-Bond (Ligand Donor) |
| C1 | CE | MET- 316 | 4.25 | 0 | Hydrophobic |
| C2 | CB | ALA- 318 | 4.2 | 0 | Hydrophobic |
| C24 | CZ2 | TRP- 320 | 3.97 | 0 | Hydrophobic |
