sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.720 Å
X-ray
2012-03-27
| Name: | Hematopoietic prostaglandin D synthase |
|---|---|
| ID: | HPGDS_HUMAN |
| AC: | O60760 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.579 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.578 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 58.27 | 41.73 |
| According to VolSite | |
| HET Code: | 9PQ |
|---|---|
| Formula: | C24H27N2O3 |
| Molecular weight: | 391.483 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.6 % |
| Polar Surface area: | 63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 21.0932 | 1.49734 | 18.0799 |
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 |
| C15 | CE | MET- 11 | 3.76 | 0 | Hydrophobic |
| O29 | N | GLY- 13 | 3.5 | 132.99 | H-Bond (Protein Donor) |
| C14 | CG | ARG- 14 | 4.41 | 0 | Hydrophobic |
| C3 | CG | ARG- 14 | 3.61 | 0 | Hydrophobic |
| C4 | CG | ARG- 14 | 3.58 | 0 | Hydrophobic |
| C6 | CG | MET- 99 | 3.52 | 0 | Hydrophobic |
| C22 | CE | MET- 99 | 3.62 | 0 | Hydrophobic |
| C5 | CB | MET- 99 | 3.25 | 0 | Hydrophobic |
| C1 | CB | MET- 99 | 3.74 | 0 | Hydrophobic |
| C17 | CD2 | TRP- 104 | 3.23 | 0 | Hydrophobic |
| C17 | CB | TRP- 104 | 3.84 | 0 | Hydrophobic |
| C22 | SG | CYS- 156 | 4.27 | 0 | Hydrophobic |
| C6 | SG | CYS- 156 | 4.32 | 0 | Hydrophobic |
| C21 | CB | THR- 159 | 3.98 | 0 | Hydrophobic |
| C28 | CG2 | THR- 159 | 3.6 | 0 | Hydrophobic |
| C28 | CB | LEU- 199 | 3.89 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 199 | 3.77 | 0 | Hydrophobic |
