sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2004-02-19
| Name: | Protoporphyrinogen oxidase, mitochondrial |
|---|---|
| ID: | PPOM_TOBAC |
| AC: | O24164 |
| Organism: | Nicotiana tabacum |
| Reign: | Eukaryota |
| TaxID: | 4097 |
| EC Number: | 1.3.3.4 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 54.880 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.998 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.55 | 55.45 |
| According to VolSite | |
| HET Code: | OMN |
|---|---|
| Formula: | C12H5BrClF4N2O2 |
| Molecular weight: | 400.531 g/mol |
| DrugBank ID: | DB03272 |
| Buried Surface Area: | 69.23 % |
| Polar Surface area: | 57.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -46.1767 | 35.1012 | 64.9416 |
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 |
| O2 | NE | ARG- 98 | 3.02 | 143.85 | H-Bond (Protein Donor) |
| CL1 | CG | ARG- 98 | 4.1 | 0 | Hydrophobic |
| F2 | CG | LEU- 334 | 4 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 334 | 3.78 | 0 | Hydrophobic |
| BR1 | CD2 | LEU- 356 | 3.96 | 0 | Hydrophobic |
| CL1 | CG | LEU- 356 | 4.27 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 356 | 3.5 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 356 | 3.5 | 0 | Hydrophobic |
| BR1 | CB | LEU- 369 | 3.74 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 369 | 4.37 | 0 | Hydrophobic |
| F3 | CB | LEU- 369 | 3.64 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 372 | 4.37 | 0 | Hydrophobic |
| F4 | CG | LEU- 372 | 4.49 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 372 | 3.71 | 0 | Hydrophobic |
| C1 | CE2 | PHE- 392 | 4.15 | 0 | Hydrophobic |
| BR1 | CD1 | PHE- 392 | 4.31 | 0 | Hydrophobic |
| C5 | CG | PHE- 392 | 3.93 | 0 | Hydrophobic |
| F2 | CD2 | PHE- 392 | 3.24 | 0 | Hydrophobic |
| F3 | CB | PHE- 392 | 3.53 | 0 | Hydrophobic |
| F4 | CD1 | PHE- 392 | 3.61 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 392 | 3.96 | 0 | Aromatic Face/Face |
| C1 | CZ | PHE- 439 | 3.99 | 0 | Hydrophobic |
| F1 | CE1 | PHE- 439 | 4.09 | 0 | Hydrophobic |
| F2 | CE1 | PHE- 439 | 4.23 | 0 | Hydrophobic |
| C1 | C6 | FAD- 610 | 3.69 | 0 | Hydrophobic |
