sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.320 Å
X-ray
2009-01-26
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 16.123 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.329 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.60 | 37.40 |
| According to VolSite | |
| HET Code: | EQU |
|---|---|
| Formula: | C18H18O2 |
| Molecular weight: | 266.334 g/mol |
| DrugBank ID: | DB03515 |
| Buried Surface Area: | 61.25 % |
| 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 |
|---|---|---|
| 24.599 | 6.87455 | -12.2721 |
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- 16 | 2.52 | 143.98 | H-Bond (Ligand Donor) |
| C6 | CG1 | VAL- 20 | 4.09 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 61 | 4.01 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 66 | 3.91 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 88 | 4.11 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 88 | 3.71 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 88 | 4.03 | 0 | Hydrophobic |
| C16 | CE | MET- 90 | 4.2 | 0 | Hydrophobic |
| C18 | CG | MET- 90 | 4.49 | 0 | Hydrophobic |
| C25 | CE | MET- 90 | 4.1 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 99 | 3.92 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 99 | 3.63 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 101 | 4.31 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 101 | 4.01 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 103 | 2.88 | 173.2 | H-Bond (Protein Donor) |
| C2 | CB | ALA- 118 | 4.13 | 0 | Hydrophobic |
| C24 | CZ2 | TRP- 120 | 3.83 | 0 | Hydrophobic |
| O1 | O | HOH- 162 | 3.27 | 140.47 | H-Bond (Protein Donor) |
