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
2008-11-30
| Name: | Prostaglandin reductase 2 |
|---|---|
| ID: | PTGR2_HUMAN |
| AC: | Q8N8N7 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.3.1.48 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.506 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.127 | 1562.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.37 | 43.63 |
| According to VolSite | |
| HET Code: | CBW |
|---|---|
| Formula: | C30H45O4 |
| Molecular weight: | 469.676 g/mol |
| DrugBank ID: | DB13089 |
| Buried Surface Area: | 63.33 % |
| Polar Surface area: | 77.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 18.4399 | -11.0425 | 24.0075 |
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 |
| C1 | CD2 | TYR- 51 | 3.48 | 0 | Hydrophobic |
| C9 | CB | TYR- 51 | 4.23 | 0 | Hydrophobic |
| C20 | CB | TYR- 51 | 4.39 | 0 | Hydrophobic |
| C27 | CB | TYR- 51 | 4.15 | 0 | Hydrophobic |
| C2 | CZ | TYR- 51 | 3.75 | 0 | Hydrophobic |
| C34 | SG | CYS- 54 | 3.74 | 0 | Hydrophobic |
| C7 | CB | TYR- 64 | 3.85 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 65 | 4.37 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 65 | 4.35 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 65 | 4.25 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 65 | 3.88 | 0 | Hydrophobic |
| C24 | CD1 | PHE- 99 | 4.13 | 0 | Hydrophobic |
| C3 | CZ | TYR- 100 | 4.39 | 0 | Hydrophobic |
| C19 | CE | MET- 135 | 4.4 | 0 | Hydrophobic |
| C24 | CE | MET- 135 | 4.48 | 0 | Hydrophobic |
| O35 | N | GLN- 255 | 2.98 | 156.15 | H-Bond (Protein Donor) |
| O34 | OH | TYR- 259 | 2.65 | 168.87 | H-Bond (Protein Donor) |
| C34 | CE1 | TYR- 259 | 3.54 | 0 | Hydrophobic |
| C22 | CB | TYR- 265 | 3.95 | 0 | Hydrophobic |
| C23 | CD1 | TYR- 265 | 3.42 | 0 | Hydrophobic |
| C28 | CZ | TYR- 265 | 4.3 | 0 | Hydrophobic |
| C28 | CG | LEU- 288 | 4.27 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 288 | 3.82 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 289 | 4.03 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 290 | 4.42 | 0 | Hydrophobic |
| C24 | CG | LEU- 290 | 3.79 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 290 | 4.17 | 0 | Hydrophobic |
| C19 | C4N | NAP- 1349 | 4.41 | 0 | Hydrophobic |
| C26 | C3N | NAP- 1349 | 4.01 | 0 | Hydrophobic |
| C28 | C3N | NAP- 1349 | 4.42 | 0 | Hydrophobic |
| O34 | O3D | NAP- 1349 | 2.69 | 157.45 | H-Bond (Protein Donor) |
