sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.610 Å
X-ray
2000-04-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.050 | 5.050 | 5.050 | 0.000 | 5.050 | 1 |
| Name: | Prostaglandin G/H synthase 1 |
|---|---|
| ID: | PGH1_SHEEP |
| AC: | P05979 |
| Organism: | Ovis aries |
| Reign: | Eukaryota |
| TaxID: | 9940 |
| EC Number: | 1.14.99.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.005 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.081 | 2710.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.71 | 56.29 |
| According to VolSite | |
| HET Code: | IBP |
|---|---|
| Formula: | C13H17O2 |
| Molecular weight: | 205.273 g/mol |
| DrugBank ID: | DB09213 |
| Buried Surface Area: | 70.08 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 68.1568 | 21.9214 | 189.707 |
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 |
| C7 | CG1 | VAL- 116 | 3.71 | 0 | Hydrophobic |
| O1 | NE | ARG- 120 | 3.47 | 126.26 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 120 | 2.7 | 151.18 | H-Bond (Protein Donor) |
| O2 | NE | ARG- 120 | 2.72 | 150.83 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 120 | 3.5 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 120 | 3.55 | 0 | Ionic (Protein Cationic) |
| C7 | CG1 | VAL- 349 | 4.14 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 349 | 3.47 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 352 | 4.19 | 0 | Hydrophobic |
| C9 | CB | SER- 353 | 3.98 | 0 | Hydrophobic |
| O1 | OH | TYR- 355 | 2.65 | 156.4 | H-Bond (Protein Donor) |
| C6 | CE1 | TYR- 355 | 3.5 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 359 | 3.78 | 0 | Hydrophobic |
| C4 | CZ | TYR- 385 | 4.13 | 0 | Hydrophobic |
| C4 | CH2 | TRP- 387 | 4.1 | 0 | Hydrophobic |
| C5 | CZ2 | TRP- 387 | 4.25 | 0 | Hydrophobic |
| C5 | CZ | PHE- 518 | 4.2 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 523 | 4.21 | 0 | Hydrophobic |
| C13 | CB | ALA- 527 | 3.65 | 0 | Hydrophobic |
| C12 | CB | SER- 530 | 4.15 | 0 | Hydrophobic |
| C4 | CB | SER- 530 | 3.74 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 531 | 4.3 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 531 | 4.17 | 0 | Hydrophobic |
