sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1999-02-11
| Name: | Scytalone dehydratase |
|---|---|
| ID: | SCYD_MAGO7 |
| AC: | P56221 |
| Organism: | Magnaporthe oryzae |
| Reign: | Eukaryota |
| TaxID: | 242507 |
| EC Number: | 4.2.1.94 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 21.083 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.370 | 398.250 |
| % Hydrophobic | % Polar |
|---|---|
| 62.71 | 37.29 |
| According to VolSite | |
| HET Code: | MS2 |
|---|---|
| Formula: | C14H16BrCl2NO2S |
| Molecular weight: | 413.157 g/mol |
| DrugBank ID: | DB04458 |
| Buried Surface Area: | 81.53 % |
| Polar Surface area: | 65.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 32.3286 | 33.5095 | 14.0058 |
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 |
| CL15 | CH2 | TRP- 26 | 3.74 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 30 | 3.88 | 0 | Hydrophobic |
| C12 | CE1 | TYR- 50 | 3.99 | 0 | Hydrophobic |
| BR1 | CE2 | PHE- 53 | 4.18 | 0 | Hydrophobic |
| C12 | CE2 | PHE- 53 | 3.47 | 0 | Hydrophobic |
| BR1 | CD2 | LEU- 54 | 3.99 | 0 | Hydrophobic |
| C3B | CE | MET- 69 | 4.44 | 0 | Hydrophobic |
| C2B | SD | MET- 69 | 4.14 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 75 | 3.61 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 75 | 3.94 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 75 | 3.59 | 0 | Hydrophobic |
| C6 | CG | LEU- 76 | 3.6 | 0 | Hydrophobic |
| CL15 | CD2 | LEU- 106 | 3.82 | 0 | Hydrophobic |
| C | CB | VAL- 108 | 3.72 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 108 | 4.34 | 0 | Hydrophobic |
| C | CB | ALA- 127 | 4.11 | 0 | Hydrophobic |
| CL16 | CB | SER- 129 | 4.09 | 0 | Hydrophobic |
| CL15 | CD1 | LEU- 147 | 3.87 | 0 | Hydrophobic |
| CL16 | CB | PRO- 149 | 3.8 | 0 | Hydrophobic |
| C12 | CG | PRO- 149 | 4 | 0 | Hydrophobic |
| CL16 | CG1 | ILE- 151 | 4.23 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 151 | 4.07 | 0 | Hydrophobic |
| C | CZ | PHE- 158 | 4.41 | 0 | Hydrophobic |
| C2A | CB | PHE- 162 | 4.31 | 0 | Hydrophobic |
| BR1 | CG | ARG- 166 | 4.47 | 0 | Hydrophobic |
| BR1 | CD2 | PHE- 169 | 4.07 | 0 | Hydrophobic |
| N1 | O | HOH- 615 | 2.94 | 155.09 | H-Bond (Ligand Donor) |
