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
2000-06-22
| 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: | 5.278 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.323 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 65.54 | 34.46 |
| According to VolSite | |
| HET Code: | AND |
|---|---|
| Formula: | C19H28O2 |
| Molecular weight: | 288.424 g/mol |
| DrugBank ID: | DB01708 |
| Buried Surface Area: | 57.67 % |
| Polar Surface area: | 37.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 13.0737 | -46.3783 | -14.4333 |
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 |
| O3 | OH | TYR- 16 | 2.64 | 169.24 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 20 | 3.83 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 56 | 3.92 | 0 | Hydrophobic |
| C2 | CE2 | TYR- 57 | 4.29 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 57 | 4.33 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 61 | 4.15 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 66 | 4.33 | 0 | Hydrophobic |
| C3 | CZ | PHE- 86 | 3.52 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 88 | 4.09 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 88 | 4.14 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 99 | 4.14 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 99 | 4.33 | 0 | Hydrophobic |
| O3 | OD2 | ASP- 103 | 2.88 | 132.31 | H-Bond (Ligand Donor) |
| C4 | CB | ALA- 118 | 4.45 | 0 | Hydrophobic |
| C7 | CE2 | TRP- 120 | 3.66 | 0 | Hydrophobic |
| C15 | CZ2 | TRP- 120 | 3.94 | 0 | Hydrophobic |
