sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2010-09-20
| 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 | 93 % |
| C | 7 % |
| B-Factor: | 43.845 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.442 | 1326.375 |
| % Hydrophobic | % Polar |
|---|---|
| 49.11 | 50.89 |
| According to VolSite | |
| HET Code: | EQU |
|---|---|
| Formula: | C18H18O2 |
| Molecular weight: | 266.334 g/mol |
| DrugBank ID: | DB03515 |
| Buried Surface Area: | 65.87 % |
| 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 |
|---|---|---|
| 7.88395 | 1.4707 | 1.42415 |
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 | 2.7 | 166.6 | H-Bond (Protein Donor) |
| C6 | CG1 | VAL- 20 | 4.09 | 0 | Hydrophobic |
| C25 | CG | PRO- 45 | 3.86 | 0 | Hydrophobic |
| C27 | CZ | PHE- 56 | 4.48 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 61 | 3.88 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 66 | 4.36 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 66 | 4.3 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 88 | 4.42 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 88 | 4.13 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 88 | 4.07 | 0 | Hydrophobic |
| C17 | CE | MET- 90 | 4.08 | 0 | Hydrophobic |
| C16 | CE | MET- 90 | 3.22 | 0 | Hydrophobic |
| C25 | CZ3 | TRP- 92 | 3.44 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 99 | 3.64 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 99 | 3.88 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 101 | 4.28 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 101 | 4.11 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 103 | 2.5 | 138.74 | H-Bond (Ligand Donor) |
| C1 | CE | MET- 116 | 4.2 | 0 | Hydrophobic |
| C2 | CB | ALA- 118 | 4.15 | 0 | Hydrophobic |
| C24 | CZ2 | TRP- 120 | 3.7 | 0 | Hydrophobic |
| C25 | CH2 | TRP- 120 | 4.43 | 0 | Hydrophobic |
