sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2000-06-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.800 | 4.800 | 4.800 | 0.000 | 4.800 | 2 |
| 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: | 11.678 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.321 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 65.52 | 34.48 |
| According to VolSite | |
| HET Code: | DXC |
|---|---|
| Formula: | C24H39O4 |
| Molecular weight: | 391.564 g/mol |
| DrugBank ID: | DB03619 |
| Buried Surface Area: | 44.96 % |
| Polar Surface area: | 80.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 3.23218 | -8.51489 | 85.2717 |
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 |
| O4 | OH | TYR- 16 | 2.62 | 155.16 | H-Bond (Protein Donor) |
| C22 | CE2 | PHE- 56 | 4.14 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 56 | 4.02 | 0 | Hydrophobic |
| C24 | CD1 | TYR- 57 | 3.8 | 0 | Hydrophobic |
| C22 | CE1 | TYR- 57 | 4.2 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 61 | 4.38 | 0 | Hydrophobic |
| C24 | CG | LEU- 61 | 4.36 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 66 | 4.33 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 88 | 4 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 88 | 3.83 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 88 | 4.31 | 0 | Hydrophobic |
| C8 | SD | MET- 90 | 4.19 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 99 | 3.72 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 99 | 3.89 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 103 | 2.72 | 157.53 | H-Bond (Protein Donor) |
| C22 | CE | MET- 116 | 4.11 | 0 | Hydrophobic |
| C2 | CH2 | TRP- 120 | 3.82 | 0 | Hydrophobic |
| C8 | CH2 | TRP- 120 | 4.22 | 0 | Hydrophobic |
