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
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 10.520 | 10.520 | 10.520 | 0.000 | 10.520 | 1 |
| 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: | 21.424 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.328 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.39 | 41.61 |
| According to VolSite | |
| HET Code: | CRP |
|---|---|
| Formula: | C15H18Cl3NO |
| Molecular weight: | 334.669 g/mol |
| DrugBank ID: | DB02946 |
| Buried Surface Area: | 80.28 % |
| Polar Surface area: | 29.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| 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 |
|---|---|---|
| 32.0442 | 33.4918 | 14.051 |
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 |
| CL1 | CH2 | TRP- 26 | 3.58 | 0 | Hydrophobic |
| C8' | CE2 | TYR- 30 | 3.81 | 0 | Hydrophobic |
| CL1 | CE2 | TYR- 30 | 4.44 | 0 | Hydrophobic |
| CL0 | CE2 | PHE- 53 | 3.97 | 0 | Hydrophobic |
| C6 | CZ | PHE- 53 | 3.34 | 0 | Hydrophobic |
| CL0 | CD2 | LEU- 54 | 4.17 | 0 | Hydrophobic |
| C3' | SD | MET- 69 | 4.28 | 0 | Hydrophobic |
| C8' | CG1 | VAL- 70 | 4.45 | 0 | Hydrophobic |
| C8' | CG1 | VAL- 75 | 3.73 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 75 | 4.01 | 0 | Hydrophobic |
| C6' | CG1 | VAL- 75 | 3.72 | 0 | Hydrophobic |
| C8' | CD1 | LEU- 76 | 3.63 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 106 | 3.99 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 108 | 3.45 | 0 | Hydrophobic |
| C4 | CB | ALA- 127 | 4.06 | 0 | Hydrophobic |
| CL2 | CB | SER- 129 | 4.16 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 147 | 4.02 | 0 | Hydrophobic |
| C5 | CB | PRO- 149 | 4.35 | 0 | Hydrophobic |
| CL2 | CB | PRO- 149 | 3.76 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 151 | 4.04 | 0 | Hydrophobic |
| CL2 | CD1 | ILE- 151 | 3.83 | 0 | Hydrophobic |
| C6 | CZ | PHE- 158 | 3.96 | 0 | Hydrophobic |
| C5' | CB | PHE- 162 | 4.37 | 0 | Hydrophobic |
| CL0 | CD2 | PHE- 169 | 4.11 | 0 | Hydrophobic |
| N | O | HOH- 629 | 3.14 | 164.83 | H-Bond (Ligand Donor) |
