sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.730 Å
X-ray
2010-06-03
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 41.116 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.821 | 293.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.72 | 48.28 |
| According to VolSite | |
| HET Code: | ASD |
|---|---|
| Formula: | C19H26O2 |
| Molecular weight: | 286.409 g/mol |
| DrugBank ID: | DB01536 |
| Buried Surface Area: | 59.29 % |
| Polar Surface area: | 34.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 3.18924 | 52.494 | 15.6561 |
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- 14 | 2.67 | 158.03 | H-Bond (Protein Donor) |
| C2 | CD1 | LEU- 18 | 4.16 | 0 | Hydrophobic |
| C19 | CZ | PHE- 54 | 4.49 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 55 | 4.44 | 0 | Hydrophobic |
| C11 | CB | SER- 58 | 4.15 | 0 | Hydrophobic |
| C19 | CB | SER- 58 | 4.43 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 63 | 4.2 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 63 | 4.23 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 63 | 4.4 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 84 | 4.15 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 84 | 3.89 | 0 | Hydrophobic |
| C16 | CZ | PHE- 86 | 3.7 | 0 | Hydrophobic |
| C14 | CE2 | PHE- 86 | 4.26 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 95 | 4.08 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 95 | 3.63 | 0 | Hydrophobic |
| C6 | CG | PRO- 97 | 3.83 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 99 | 3.04 | 152.31 | H-Bond (Protein Donor) |
| C15 | CE1 | PHE- 116 | 4.35 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 116 | 3.49 | 0 | Hydrophobic |
| C7 | CZ | PHE- 116 | 3.89 | 0 | Hydrophobic |
