sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2010-01-27
| Name: | Prostaglandin-H2 D-isomerase |
|---|---|
| ID: | PTGDS_MOUSE |
| AC: | O09114 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 5.3.99.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.477 | 1059.750 |
| % Hydrophobic | % Polar |
|---|---|
| 54.14 | 45.86 |
| According to VolSite | |
| HET Code: | PUC |
|---|---|
| Formula: | C21H33O4 |
| Molecular weight: | 349.484 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 45.42 % |
| Polar Surface area: | 69.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -5.17088 | 2.89008 | -4.29296 |
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 |
| C11 | CB | SER- 45 | 4.38 | 0 | Hydrophobic |
| C21 | CB | SER- 45 | 3.65 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 48 | 4.25 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 48 | 3.97 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 55 | 4.14 | 0 | Hydrophobic |
| C4 | CB | LEU- 62 | 3.31 | 0 | Hydrophobic |
| C7 | CB | LEU- 62 | 4.4 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 62 | 3.2 | 0 | Hydrophobic |
| C21 | SG | CYS- 65 | 3.34 | 0 | Hydrophobic |
| O3 | OG | SER- 81 | 3.23 | 162.61 | H-Bond (Ligand Donor) |
| C3 | CG | GLU- 90 | 3.63 | 0 | Hydrophobic |
| C17 | SD | MET- 94 | 4.21 | 0 | Hydrophobic |
| C19 | CZ | TYR- 107 | 3.83 | 0 | Hydrophobic |
| C20 | CB | SER- 109 | 3.85 | 0 | Hydrophobic |
| C20 | CG | PRO- 110 | 3.9 | 0 | Hydrophobic |
