sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2008-03-21
| 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: | 12.376 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.284 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 58.47 | 41.53 |
| According to VolSite | |
| HET Code: | PDN |
|---|---|
| Formula: | C21H26O5 |
| Molecular weight: | 358.428 g/mol |
| DrugBank ID: | DB00635 |
| Buried Surface Area: | 61.17 % |
| Polar Surface area: | 94.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 4.55881 | 18.6128 | -33.0569 |
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 |
| C6 | CD1 | TYR- 26 | 4.04 | 0 | Hydrophobic |
| C7 | CZ | TYR- 26 | 3.46 | 0 | Hydrophobic |
| C15 | CZ | TYR- 26 | 4.37 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 57 | 4.24 | 0 | Hydrophobic |
| O1 | OH | TYR- 58 | 2.83 | 154.14 | H-Bond (Protein Donor) |
| C2 | CZ3 | TRP- 89 | 3.71 | 0 | Hydrophobic |
| C2 | CG | GLU- 120 | 3.82 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 132 | 3.71 | 0 | Hydrophobic |
| C21 | CD1 | TYR- 132 | 4.27 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 140 | 4.27 | 0 | Hydrophobic |
| C6 | CH2 | TRP- 230 | 4.26 | 0 | Hydrophobic |
| C8 | CE3 | TRP- 230 | 4.29 | 0 | Hydrophobic |
| C15 | CD2 | TRP- 230 | 3.74 | 0 | Hydrophobic |
| C16 | CB | TRP- 230 | 3.97 | 0 | Hydrophobic |
| C18 | CB | TRP- 230 | 3.57 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 309 | 4.31 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 311 | 3.86 | 0 | Hydrophobic |
| C12 | CE | MET- 313 | 4.39 | 0 | Hydrophobic |
| C18 | CE | MET- 313 | 3.8 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 314 | 3.82 | 0 | Hydrophobic |
| C2 | C3N | NAP- 943 | 4.4 | 0 | Hydrophobic |
| C6 | C5N | NAP- 943 | 4.23 | 0 | Hydrophobic |
| C19 | C4N | NAP- 943 | 4.12 | 0 | Hydrophobic |
