sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2003-06-12
| Name: | Peroxisomal hydratase-dehydrogenase-epimerase |
|---|---|
| ID: | FOX2_CANTR |
| AC: | P22414 |
| Organism: | Candida tropicalis |
| Reign: | Eukaryota |
| TaxID: | 5482 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 15.847 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.855 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.03 | 51.97 |
| According to VolSite | |
| HET Code: | HDC |
|---|---|
| Formula: | C31H50N7O18P3S |
| Molecular weight: | 933.751 g/mol |
| DrugBank ID: | DB03192 |
| Buried Surface Area: | 48.14 % |
| 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 |
|---|---|---|
| -138.534 | 38.0666 | -5.6751 |
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 |
| C5' | CZ | PHE- 50 | 4.24 | 0 | Hydrophobic |
| C6' | CE1 | PHE- 50 | 3.74 | 0 | Hydrophobic |
| C10 | CB | GLN- 56 | 4.22 | 0 | Hydrophobic |
| C8' | CE2 | PHE- 59 | 4.04 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 71 | 4.24 | 0 | Hydrophobic |
| C7' | CD2 | LEU- 71 | 3.84 | 0 | Hydrophobic |
| CDP | CD1 | LEU- 72 | 3.88 | 0 | Hydrophobic |
| CEP | CD1 | LEU- 72 | 4.08 | 0 | Hydrophobic |
| S1P | CD2 | LEU- 72 | 3.73 | 0 | Hydrophobic |
| N4P | O | HIS- 73 | 2.94 | 144.43 | H-Bond (Ligand Donor) |
| S1P | CB | HIS- 73 | 4.28 | 0 | Hydrophobic |
| C2' | CB | HIS- 73 | 4 | 0 | Hydrophobic |
| N6A | O | GLY- 74 | 3.07 | 152.87 | H-Bond (Ligand Donor) |
| C4B | CB | LYS- 103 | 4.09 | 0 | Hydrophobic |
| C3B | CD | LYS- 103 | 4.45 | 0 | Hydrophobic |
| O9A | NZ | LYS- 103 | 3.01 | 173.81 | H-Bond (Protein Donor) |
| O9A | NZ | LYS- 103 | 3.01 | 0 | Ionic (Protein Cationic) |
| C5' | CE1 | TYR- 131 | 4.08 | 0 | Hydrophobic |
| C7' | CZ | TYR- 131 | 4.21 | 0 | Hydrophobic |
| CEP | CG | PHE- 132 | 3.74 | 0 | Hydrophobic |
| CCP | CZ | PHE- 132 | 3.86 | 0 | Hydrophobic |
| C1B | CE2 | PHE- 132 | 4.17 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 182 | 2.73 | 157.42 | H-Bond (Ligand Donor) |
| O2' | ND2 | ASN- 184 | 2.97 | 161.02 | H-Bond (Protein Donor) |
| S1P | CD2 | LEU- 186 | 3.98 | 0 | Hydrophobic |
| O2' | NE2 | GLN- 187 | 3 | 139.79 | H-Bond (Protein Donor) |
| C2P | CD1 | ILE- 202 | 3.71 | 0 | Hydrophobic |
| O1' | N | GLY- 205 | 3.12 | 171.55 | H-Bond (Protein Donor) |
| DuAr | CZ | ARG- 229 | 3.67 | 18.91 | Pi/Cation |
| N8P | O | PHE- 230 | 2.89 | 134.69 | H-Bond (Ligand Donor) |
| C6P | CB | PHE- 230 | 4.02 | 0 | Hydrophobic |
| C6P | CG2 | ILE- 233 | 4.34 | 0 | Hydrophobic |
| O1' | O | HOH- 3299 | 2.63 | 179.96 | H-Bond (Protein Donor) |
