sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.640 Å
X-ray
1994-03-28
| Name: | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase |
|---|---|
| ID: | HSD_STREX |
| AC: | P19992 |
| Organism: | Streptomyces exfoliatus |
| Reign: | Bacteria |
| TaxID: | 1905 |
| EC Number: | 1.1.1.53 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 11.441 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.428 | 1272.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.30 | 55.70 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.07 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 61.99 | 11.7351 | 66.3517 |
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 |
| C3B | CG | ARG- 16 | 3.93 | 0 | Hydrophobic |
| O2N | N | LEU- 18 | 3.02 | 129.37 | H-Bond (Protein Donor) |
| O3B | OD2 | ASP- 37 | 2.98 | 130.89 | H-Bond (Ligand Donor) |
| O3B | OD1 | ASP- 37 | 3.32 | 148.11 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 37 | 3.5 | 156.71 | H-Bond (Ligand Donor) |
| C3B | CD2 | LEU- 39 | 4.25 | 0 | Hydrophobic |
| N6A | OD1 | ASP- 60 | 2.92 | 146.67 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 61 | 3.01 | 152.66 | H-Bond (Protein Donor) |
| C1B | CB | ALA- 88 | 4.12 | 0 | Hydrophobic |
| C2D | CG2 | ILE- 137 | 4.35 | 0 | Hydrophobic |
| O2D | O | SER- 138 | 3.02 | 138.68 | H-Bond (Ligand Donor) |
| C5N | CB | SER- 139 | 3.51 | 0 | Hydrophobic |
| C2D | CZ | TYR- 152 | 4.12 | 0 | Hydrophobic |
| O3D | NZ | LYS- 156 | 3.04 | 147.59 | H-Bond (Protein Donor) |
| C5N | CB | PRO- 182 | 4.26 | 0 | Hydrophobic |
