sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2009-12-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.700 | 7.860 | 7.860 | 0.160 | 8.020 | 2 |
| 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: | 29.516 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.534 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 47.06 | 52.94 |
| According to VolSite | |
| HET Code: | KXO |
|---|---|
| Formula: | C19H19F4N3O |
| Molecular weight: | 381.367 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.25 % |
| Polar Surface area: | 45.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 22.1053 | -0.0699259 | 17.7338 |
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 |
| C9 | CD1 | PHE- 9 | 3.87 | 0 | Hydrophobic |
| F26 | CZ | PHE- 9 | 3.42 | 0 | Hydrophobic |
| C15 | SD | MET- 11 | 4.35 | 0 | Hydrophobic |
| C9 | SD | MET- 11 | 3.71 | 0 | Hydrophobic |
| C5 | CG | ARG- 14 | 4.13 | 0 | Hydrophobic |
| C2 | CG | ARG- 14 | 3.37 | 0 | Hydrophobic |
| F25 | CG | GLN- 36 | 3.98 | 0 | Hydrophobic |
| F26 | CE2 | TRP- 39 | 3.62 | 0 | Hydrophobic |
| F24 | CE | MET- 99 | 3.64 | 0 | Hydrophobic |
| C1 | CB | MET- 99 | 3.7 | 0 | Hydrophobic |
| C8 | CB | TRP- 104 | 3.9 | 0 | Hydrophobic |
| C4 | CB | TRP- 104 | 3.99 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 104 | 3.83 | 0 | Aromatic Face/Face |
| C8 | CB | ALA- 105 | 4.31 | 0 | Hydrophobic |
| F24 | CG2 | ILE- 155 | 3.9 | 0 | Hydrophobic |
| F24 | SG | CYS- 156 | 3.84 | 0 | Hydrophobic |
| F24 | CB | THR- 159 | 4.31 | 0 | Hydrophobic |
