sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2014-01-07
| Name: | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial |
|---|---|
| ID: | COQ5_YEAST |
| AC: | P49017 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.968 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.889 | 745.875 |
| % Hydrophobic | % Polar |
|---|---|
| 47.51 | 52.49 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 69.44 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -35.8795 | -37.1941 | 28.4944 |
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 |
| SD | CG | TYR- 78 | 4.22 | 0 | Hydrophobic |
| CE | CD1 | TYR- 78 | 3.44 | 0 | Hydrophobic |
| C3' | CE2 | TYR- 78 | 3.77 | 0 | Hydrophobic |
| OXT | NZ | LYS- 94 | 3.35 | 135.19 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 119 | 4.29 | 0 | Hydrophobic |
| C1' | CB | ALA- 119 | 3.83 | 0 | Hydrophobic |
| N | OG | SER- 122 | 3.19 | 138.75 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 148 | 3.05 | 171.49 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 148 | 2.58 | 145.64 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 149 | 3.43 | 155.3 | H-Bond (Protein Donor) |
| C3' | CG | MET- 153 | 4.41 | 0 | Hydrophobic |
| N6 | OD1 | ASN- 179 | 2.98 | 151.27 | H-Bond (Ligand Donor) |
| N1 | N | GLY- 180 | 2.85 | 160.61 | H-Bond (Protein Donor) |
| OXT | OG | SER- 197 | 2.96 | 151.86 | H-Bond (Protein Donor) |
| O | O | HOH- 778 | 3.26 | 130 | H-Bond (Protein Donor) |
