sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2005-08-30
| Name: | Prostaglandin reductase 3 |
|---|---|
| ID: | ZADH2_HUMAN |
| AC: | Q8N4Q0 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 98 % |
| B | 2 % |
| B-Factor: | 13.804 |
|---|---|
| Number of residues: | 56 |
| Including | |
| Standard Amino Acids: | 52 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.259 | 1447.875 |
| % Hydrophobic | % Polar |
|---|---|
| 54.55 | 45.45 |
| According to VolSite | |
| HET Code: | NAP |
|---|---|
| Formula: | C21H25N7O17P3 |
| Molecular weight: | 740.381 g/mol |
| DrugBank ID: | DB03461 |
| Buried Surface Area: | 67.16 % |
| Polar Surface area: | 405.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 42.3 | 11.86 | -0.744667 |
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 |
| O1N | N | ALA- 67 | 3.02 | 172.38 | H-Bond (Protein Donor) |
| C5D | CB | ALA- 67 | 4.5 | 0 | Hydrophobic |
| C3D | CB | ALA- 67 | 3.8 | 0 | Hydrophobic |
| C5N | CG1 | VAL- 146 | 3.79 | 0 | Hydrophobic |
| C4N | CG2 | THR- 150 | 3.71 | 0 | Hydrophobic |
| C4B | CB | ALA- 171 | 4.18 | 0 | Hydrophobic |
| O1A | N | GLY- 175 | 2.79 | 161.48 | H-Bond (Protein Donor) |
| O2N | N | THR- 176 | 3.27 | 162.96 | H-Bond (Protein Donor) |
| C5D | CG2 | THR- 176 | 3.99 | 0 | Hydrophobic |
| O3B | NZ | LYS- 200 | 3.46 | 123.09 | H-Bond (Protein Donor) |
| O3X | NZ | LYS- 200 | 2.68 | 157.34 | H-Bond (Protein Donor) |
| O3X | NZ | LYS- 200 | 2.68 | 0 | Ionic (Protein Cationic) |
| O2X | OH | TYR- 215 | 2.54 | 166.58 | H-Bond (Protein Donor) |
| O3D | O | SER- 238 | 3.03 | 148.11 | H-Bond (Ligand Donor) |
| C4D | CB | SER- 238 | 3.53 | 0 | Hydrophobic |
| C3N | CG2 | ILE- 260 | 4.25 | 0 | Hydrophobic |
| N7N | O | ILE- 260 | 2.92 | 167.39 | H-Bond (Ligand Donor) |
| C1B | CG2 | ILE- 263 | 4.41 | 0 | Hydrophobic |
| C3D | CB | ILE- 263 | 4.32 | 0 | Hydrophobic |
| C5B | CD1 | ILE- 263 | 3.49 | 0 | Hydrophobic |
| O3D | OH | TYR- 266 | 3.05 | 121.9 | H-Bond (Protein Donor) |
| O2D | OH | TYR- 266 | 2.72 | 158.85 | H-Bond (Protein Donor) |
| C3D | CE2 | TYR- 266 | 4.14 | 0 | Hydrophobic |
| N7N | O | PHE- 294 | 2.78 | 150.87 | H-Bond (Ligand Donor) |
| O7N | N | LEU- 296 | 3 | 164.33 | H-Bond (Protein Donor) |
| C5B | CG | MET- 347 | 3.67 | 0 | Hydrophobic |
| O1A | ND2 | ASN- 352 | 2.83 | 139.33 | H-Bond (Protein Donor) |
| O3B | OD1 | ASN- 352 | 2.65 | 151.34 | H-Bond (Ligand Donor) |
| O1N | O | HOH- 2073 | 2.81 | 165.27 | H-Bond (Protein Donor) |
| O2A | O | HOH- 2188 | 2.71 | 179.99 | H-Bond (Protein Donor) |
| O3B | O | HOH- 2353 | 2.65 | 155.93 | H-Bond (Protein Donor) |
