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
2011-09-21
| 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: | 19.915 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.163 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.59 | 37.41 |
| According to VolSite | |
| HET Code: | CBD |
|---|---|
| Formula: | C29H17ClN7O11S3 |
| Molecular weight: | 771.134 g/mol |
| DrugBank ID: | DB02633 |
| Buried Surface Area: | 44.48 % |
| Polar Surface area: | 331.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 5 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 13.7262 | 3.86784 | 76.9483 |
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 |
| CD4 | CE | MET- 11 | 4.1 | 0 | Hydrophobic |
| CB3 | SD | MET- 11 | 4.18 | 0 | Hydrophobic |
| C2 | CD | ARG- 14 | 4.04 | 0 | Hydrophobic |
| C5 | CG | ARG- 14 | 4.26 | 0 | Hydrophobic |
| C3 | CG | ARG- 14 | 3.8 | 0 | Hydrophobic |
| O4 | NE | ARG- 14 | 2.7 | 134.09 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 14 | 2.56 | 139.69 | H-Bond (Protein Donor) |
| C5 | CB | MET- 99 | 4.05 | 0 | Hydrophobic |
| C6 | CG | MET- 99 | 3.58 | 0 | Hydrophobic |
| C8 | CE | MET- 99 | 3.82 | 0 | Hydrophobic |
| C14 | CB | TRP- 104 | 3.52 | 0 | Hydrophobic |
| CB5 | CB | TRP- 104 | 3.92 | 0 | Hydrophobic |
| CL | CB | ALA- 105 | 4.42 | 0 | Hydrophobic |
| CL | CD | LYS- 107 | 3.48 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 155 | 4.12 | 0 | Hydrophobic |
| C7 | SG | CYS- 156 | 3.55 | 0 | Hydrophobic |
| C9 | CB | THR- 159 | 4.42 | 0 | Hydrophobic |
| O3D | NZ | LYS- 198 | 3.35 | 160.54 | H-Bond (Protein Donor) |
| O3D | NZ | LYS- 198 | 3.35 | 0 | Ionic (Protein Cationic) |
| CD6 | CB | LYS- 198 | 4.35 | 0 | Hydrophobic |
| CB3 | CD1 | LEU- 199 | 3.35 | 0 | Hydrophobic |
| CB4 | CG | LEU- 199 | 4.28 | 0 | Hydrophobic |
| CB5 | CD1 | LEU- 199 | 4.24 | 0 | Hydrophobic |
| CD6 | CD1 | LEU- 199 | 4.42 | 0 | Hydrophobic |
