sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
1999-02-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 10.490 | 10.490 | 10.490 | 0.000 | 10.490 | 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 |
|---|---|
| A | 100 % |
| B-Factor: | 18.485 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.459 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 65.95 | 34.05 |
| According to VolSite | |
| HET Code: | UNN |
|---|---|
| Formula: | C23H19F2N3 |
| Molecular weight: | 375.414 g/mol |
| DrugBank ID: | DB03678 |
| Buried Surface Area: | 78.33 % |
| Polar Surface area: | 37.81 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 27.9487 | 11.0546 | 33.1373 |
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 |
| C31 | CE2 | TYR- 30 | 4.45 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 53 | 3.98 | 0 | Aromatic Face/Face |
| C23 | CB | PHE- 53 | 3.67 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 54 | 4.42 | 0 | Hydrophobic |
| C17 | CE | MET- 69 | 4.28 | 0 | Hydrophobic |
| C18 | CG | MET- 69 | 4.17 | 0 | Hydrophobic |
| C19 | CE | MET- 69 | 3.63 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 70 | 4.23 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 75 | 3.66 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 75 | 3.66 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 75 | 4.1 | 0 | Hydrophobic |
| C31 | CG | LEU- 76 | 4.07 | 0 | Hydrophobic |
| F29 | CB | LEU- 106 | 4.21 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 106 | 3.57 | 0 | Hydrophobic |
| F28 | CB | VAL- 108 | 3.46 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 108 | 3.4 | 0 | Hydrophobic |
| F29 | CB | ALA- 127 | 3.77 | 0 | Hydrophobic |
| C3 | CB | SER- 129 | 4.01 | 0 | Hydrophobic |
| N6 | ND2 | ASN- 131 | 3.21 | 176.3 | H-Bond (Protein Donor) |
| C4 | CB | PRO- 149 | 4.41 | 0 | Hydrophobic |
| C24 | CG | PRO- 149 | 3.75 | 0 | Hydrophobic |
| F29 | CG1 | ILE- 151 | 4.07 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 151 | 3.44 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 151 | 3.72 | 0 | Hydrophobic |
| F28 | CZ | PHE- 158 | 3.52 | 0 | Hydrophobic |
| C12 | CZ | PHE- 162 | 4.34 | 0 | Hydrophobic |
| C16 | CB | PHE- 162 | 4.33 | 0 | Hydrophobic |
| N11 | O | HOH- 538 | 2.53 | 158.53 | H-Bond (Ligand Donor) |
