sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2010-03-17
| Name: | Steroid Delta-isomerase |
|---|---|
| ID: | SDIS_COMTE |
| AC: | P00947 |
| Organism: | Comamonas testosteroni |
| Reign: | Bacteria |
| TaxID: | 285 |
| EC Number: | 5.3.3.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 15 % |
| D | 85 % |
| B-Factor: | 22.813 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.196 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.99 | 37.01 |
| According to VolSite | |
| HET Code: | EQU |
|---|---|
| Formula: | C18H18O2 |
| Molecular weight: | 266.334 g/mol |
| DrugBank ID: | DB03515 |
| Buried Surface Area: | 78.83 % |
| 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 |
|---|---|---|
| 26.6302 | -14.5632 | 64.1451 |
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 |
| C25 | CZ | TYR- 14 | 4.16 | 0 | Hydrophobic |
| O26 | OH | TYR- 14 | 2.64 | 162.51 | H-Bond (Protein Donor) |
| C24 | CD2 | LEU- 18 | 4.03 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 18 | 3.49 | 0 | Hydrophobic |
| C27 | CZ | PHE- 54 | 3.64 | 0 | Hydrophobic |
| C25 | CE1 | TYR- 55 | 4.12 | 0 | Hydrophobic |
| C24 | CB | SER- 58 | 4.34 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 63 | 4.44 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 63 | 4.28 | 0 | Hydrophobic |
| C18 | CZ | PHE- 82 | 4.06 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 84 | 4.39 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 84 | 3.77 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 84 | 4.43 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 84 | 3.64 | 0 | Hydrophobic |
| C1 | CB | GLN- 89 | 3.94 | 0 | Hydrophobic |
| C3 | CG | GLN- 89 | 3.58 | 0 | Hydrophobic |
| C10 | CG | GLN- 89 | 3.51 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 95 | 3.74 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 95 | 3.7 | 0 | Hydrophobic |
| C18 | CG | PRO- 97 | 4 | 0 | Hydrophobic |
| O26 | ND2 | ASN- 99 | 3.07 | 145.87 | H-Bond (Protein Donor) |
| C18 | CB | ALA- 114 | 4.25 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 116 | 3.75 | 0 | Hydrophobic |
| C5 | CZ | PHE- 116 | 3.24 | 0 | Hydrophobic |
