sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2015-07-26
| Name: | Peroxisomal bifunctional enzyme |
|---|---|
| ID: | ECHP_RAT |
| AC: | P07896 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 1.1.1.35 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 50.317 |
|---|---|
| Number of residues: | 53 |
| Including | |
| Standard Amino Acids: | 51 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.065 | 884.250 |
| % Hydrophobic | % Polar |
|---|---|
| 55.73 | 44.27 |
| According to VolSite | |
| HET Code: | HSC |
|---|---|
| Formula: | C31H50N7O18P3S |
| Molecular weight: | 933.751 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.53 % |
| Polar Surface area: | 449.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 23 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 28 |
| X | Y | Z |
|---|---|---|
| -44.1663 | 20.2471 | -22.3671 |
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 |
| C1B | CG | PRO- 20 | 4.5 | 0 | Hydrophobic |
| C4B | CG | PRO- 20 | 3.94 | 0 | Hydrophobic |
| CDP | CG1 | VAL- 21 | 3.74 | 0 | Hydrophobic |
| C5B | CG1 | VAL- 21 | 3.95 | 0 | Hydrophobic |
| N4P | O | ALA- 59 | 2.85 | 169.7 | H-Bond (Ligand Donor) |
| CDP | CB | ALA- 59 | 3.71 | 0 | Hydrophobic |
| O1 | N | ALA- 61 | 2.86 | 161.94 | H-Bond (Protein Donor) |
| C2 | CB | ALA- 61 | 3.83 | 0 | Hydrophobic |
| S1P | CB | ALA- 61 | 4.32 | 0 | Hydrophobic |
| N6A | O | ALA- 61 | 3.19 | 155.37 | H-Bond (Ligand Donor) |
| N1A | N | ILE- 63 | 3.03 | 172.64 | H-Bond (Protein Donor) |
| C2 | CZ | PHE- 66 | 3.93 | 0 | Hydrophobic |
| S1P | CZ | PHE- 66 | 3.65 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 73 | 3.6 | 0 | Hydrophobic |
| C6 | CB | LEU- 75 | 4.47 | 0 | Hydrophobic |
| CDP | CG1 | VAL- 96 | 4.44 | 0 | Hydrophobic |
| CEP | CG2 | VAL- 96 | 3.71 | 0 | Hydrophobic |
| C6P | CD1 | LEU- 98 | 3.83 | 0 | Hydrophobic |
| CEP | CD1 | LEU- 98 | 3.56 | 0 | Hydrophobic |
| O1 | N | GLY- 100 | 2.98 | 148.2 | H-Bond (Protein Donor) |
| C6P | CG | PRO- 122 | 3.75 | 0 | Hydrophobic |
| C2 | CG | GLU- 123 | 3.97 | 0 | Hydrophobic |
| S1P | CG | GLU- 123 | 3.83 | 0 | Hydrophobic |
| C2P | CD1 | LEU- 126 | 3.77 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 128 | 4.35 | 0 | Hydrophobic |
| S1P | CD1 | ILE- 128 | 3.85 | 0 | Hydrophobic |
| O3 | N | GLY- 131 | 3.42 | 135.68 | H-Bond (Protein Donor) |
| C4 | CB | ALA- 132 | 4.09 | 0 | Hydrophobic |
| C6 | CB | ALA- 132 | 4.32 | 0 | Hydrophobic |
| O9P | OH | TYR- 156 | 2.65 | 165.28 | H-Bond (Protein Donor) |
| C10 | CG | GLU- 252 | 3.84 | 0 | Hydrophobic |
| C2 | CE1 | PHE- 255 | 4.44 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 255 | 3.9 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 255 | 3.43 | 0 | Hydrophobic |
| C10 | CD2 | PHE- 255 | 4.37 | 0 | Hydrophobic |
| C5 | CZ | PHE- 255 | 3.57 | 0 | Hydrophobic |
| C10 | CE | MET- 256 | 4.22 | 0 | Hydrophobic |
| O1A | NZ | LYS- 275 | 3.74 | 0 | Ionic (Protein Cationic) |
| C2B | CG | LYS- 275 | 4.15 | 0 | Hydrophobic |
| C3B | CD | LYS- 275 | 4.43 | 0 | Hydrophobic |
| O7A | NZ | LYS- 279 | 3.73 | 0 | Ionic (Protein Cationic) |
| O9A | NZ | LYS- 279 | 3.44 | 0 | Ionic (Protein Cationic) |
| O9A | NZ | LYS- 279 | 3.44 | 147.04 | H-Bond (Protein Donor) |
