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
2008-02-20
| Name: | 3-oxo-5-beta-steroid 4-dehydrogenase |
|---|---|
| ID: | AK1D1_HUMAN |
| AC: | P51857 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 14.873 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.951 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.29 | 45.71 |
| According to VolSite | |
| HET Code: | ASD |
|---|---|
| Formula: | C19H26O2 |
| Molecular weight: | 286.409 g/mol |
| DrugBank ID: | DB01536 |
| Buried Surface Area: | 70.37 % |
| 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 |
|---|---|---|
| 14.0295 | 39.2757 | 62.9531 |
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 |
| C11 | CZ | TYR- 26 | 3.6 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 26 | 4.26 | 0 | Hydrophobic |
| C19 | CD2 | TYR- 26 | 3.4 | 0 | Hydrophobic |
| C1 | CE2 | TYR- 26 | 3.72 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 57 | 4.38 | 0 | Hydrophobic |
| C18 | CE2 | TYR- 58 | 3.88 | 0 | Hydrophobic |
| C16 | CH2 | TRP- 89 | 3.88 | 0 | Hydrophobic |
| O2 | OH | TYR- 132 | 2.74 | 154.06 | H-Bond (Protein Donor) |
| C2 | CB | ASN- 227 | 3.6 | 0 | Hydrophobic |
| O1 | N | ASN- 227 | 2.92 | 162.46 | H-Bond (Protein Donor) |
| C1 | CB | TRP- 230 | 4.39 | 0 | Hydrophobic |
| C11 | CE2 | TRP- 230 | 4.21 | 0 | Hydrophobic |
| C12 | CZ2 | TRP- 230 | 3.76 | 0 | Hydrophobic |
| C13 | CH2 | TRP- 230 | 4.37 | 0 | Hydrophobic |
| C14 | CZ3 | TRP- 230 | 3.95 | 0 | Hydrophobic |
| C16 | CZ3 | TRP- 230 | 4.27 | 0 | Hydrophobic |
| C6 | CB | TRP- 230 | 4.47 | 0 | Hydrophobic |
| C9 | CD2 | TRP- 230 | 3.86 | 0 | Hydrophobic |
| C7 | CE3 | TRP- 230 | 4.15 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 309 | 3.64 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 311 | 4.41 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 311 | 4.29 | 0 | Hydrophobic |
| C16 | CH2 | TRP- 314 | 4.05 | 0 | Hydrophobic |
| C15 | C4N | NAP- 327 | 4.15 | 0 | Hydrophobic |
| C19 | C5N | NAP- 327 | 3.88 | 0 | Hydrophobic |
| C8 | C5N | NAP- 327 | 3.7 | 0 | Hydrophobic |
