sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2013-01-23
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.770 | 5.770 | 5.770 | 0.000 | 5.770 | 1 |
| Name: | Protoporphyrinogen oxidase |
|---|---|
| ID: | PPOX_HUMAN |
| AC: | P50336 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.3.3.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 19.747 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.155 | 978.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.34 | 49.66 |
| According to VolSite | |
| HET Code: | ACJ |
|---|---|
| Formula: | C14H6ClF3NO5 |
| Molecular weight: | 360.649 g/mol |
| DrugBank ID: | DB07338 |
| Buried Surface Area: | 73.51 % |
| Polar Surface area: | 95.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 17.6187 | -23.7611 | -45.3763 |
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 |
| O4 | CZ | ARG- 97 | 3.24 | 0 | Ionic (Protein Cationic) |
| F1 | CB | ALA- 172 | 3.6 | 0 | Hydrophobic |
| F3 | CG1 | VAL- 314 | 4.25 | 0 | Hydrophobic |
| C10 | CE2 | PHE- 331 | 3.48 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 334 | 3.56 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 334 | 3.44 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 334 | 3.56 | 0 | Hydrophobic |
| CL1 | CB | LEU- 344 | 3.53 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 347 | 3.65 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 347 | 4.1 | 0 | Hydrophobic |
| CL1 | CB | MET- 368 | 4.14 | 0 | Hydrophobic |
| C7 | CG | MET- 368 | 3.53 | 0 | Hydrophobic |
| F3 | CG1 | ILE- 419 | 4.5 | 0 | Hydrophobic |
| F3 | C7 | FAD- 502 | 3.74 | 0 | Hydrophobic |
| F2 | C6 | FAD- 502 | 3.41 | 0 | Hydrophobic |
