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
1997-06-12
| Name: | Peroxisomal (S)-2-hydroxy-acid oxidase |
|---|---|
| ID: | GOX_SPIOL |
| AC: | P05414 |
| Organism: | Spinacia oleracea |
| Reign: | Eukaryota |
| TaxID: | 3562 |
| EC Number: | 1.1.3.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.051 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.214 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 58.60 | 41.40 |
| According to VolSite | |
| HET Code: | HST |
|---|---|
| Formula: | C14H24N3O2S |
| Molecular weight: | 298.424 g/mol |
| DrugBank ID: | DB04374 |
| Buried Surface Area: | 63.47 % |
| Polar Surface area: | 107 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 45.9177 | 55.2969 | 18.4579 |
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 | OH | TYR- 24 | 2.79 | 132.86 | H-Bond (Protein Donor) |
| S | CZ | TYR- 24 | 4.25 | 0 | Hydrophobic |
| C2 | CE1 | TYR- 24 | 4.27 | 0 | Hydrophobic |
| S | CB | ALA- 79 | 3.74 | 0 | Hydrophobic |
| C7 | CE2 | TRP- 108 | 3.67 | 0 | Hydrophobic |
| C11 | CH2 | TRP- 108 | 3.5 | 0 | Hydrophobic |
| N2 | OH | TYR- 129 | 2.85 | 167.43 | H-Bond (Protein Donor) |
| C10 | CE2 | TYR- 129 | 3.64 | 0 | Hydrophobic |
| C11 | CD2 | TYR- 129 | 3.48 | 0 | Hydrophobic |
| C11 | CE1 | TYR- 131 | 3.6 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 161 | 3.55 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 161 | 3.92 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 161 | 4.45 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 164 | 2.91 | 141.58 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 164 | 3.02 | 137.08 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 164 | 3.26 | 153.24 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 164 | 3.37 | 0 | Ionic (Protein Cationic) |
| C1 | CD2 | PHE- 172 | 3.86 | 0 | Hydrophobic |
| C2 | CE2 | PHE- 172 | 3.56 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 207 | 3.47 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 207 | 3.63 | 0 | Hydrophobic |
| N3 | NE2 | HIS- 254 | 2.7 | 161.56 | H-Bond (Ligand Donor) |
| O1 | NH2 | ARG- 257 | 3.23 | 147.65 | H-Bond (Protein Donor) |
| O1 | NE | ARG- 257 | 3.2 | 152.35 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 257 | 2.85 | 147.33 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 257 | 3.66 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 257 | 3.96 | 0 | Ionic (Protein Cationic) |
