sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2010-06-21
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 23.046 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.064 | 1063.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.62 | 52.38 |
| According to VolSite | |
| HET Code: | ACJ |
|---|---|
| Formula: | C14H6ClF3NO5 |
| Molecular weight: | 360.649 g/mol |
| DrugBank ID: | DB07338 |
| Buried Surface Area: | 72.56 % |
| 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 |
|---|---|---|
| -29.6298 | 3.33329 | 45.335 |
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 |
| O5 | CZ | ARG- 97 | 3.66 | 0 | Ionic (Protein Cationic) |
| F1 | CB | ALA- 172 | 3.22 | 0 | Hydrophobic |
| F3 | CG2 | VAL- 314 | 4.09 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 334 | 3.97 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 334 | 3.66 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 334 | 3.76 | 0 | Hydrophobic |
| CL1 | CB | LEU- 344 | 3.3 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 344 | 4.49 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 347 | 3.68 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 347 | 4.29 | 0 | Hydrophobic |
| CL1 | CB | MET- 368 | 3.98 | 0 | Hydrophobic |
| C7 | CG | MET- 368 | 3.6 | 0 | Hydrophobic |
| C6 | CE | MET- 368 | 3.89 | 0 | Hydrophobic |
| C3 | CG | MET- 368 | 4.12 | 0 | Hydrophobic |
| F3 | CG1 | ILE- 419 | 4.41 | 0 | Hydrophobic |
| F1 | CD1 | ILE- 419 | 3.25 | 0 | Hydrophobic |
| F3 | C7 | FAD- 479 | 3.44 | 0 | Hydrophobic |
| F2 | C6 | FAD- 479 | 3.73 | 0 | Hydrophobic |
