sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.840 Å
X-ray
2016-05-05
| Name: | Carminomycin 4-O-methyltransferase DnrK |
|---|---|
| ID: | DNRK_STRPE |
| AC: | Q06528 |
| Organism: | Streptomyces peucetius |
| Reign: | Bacteria |
| TaxID: | 1950 |
| EC Number: | 2.1.1.292 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 31.716 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 17 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.962 | 1630.125 |
| % Hydrophobic | % Polar |
|---|---|
| 56.31 | 43.69 |
| According to VolSite | |
| HET Code: | 4MU |
|---|---|
| Formula: | C10H8O3 |
| Molecular weight: | 176.169 g/mol |
| DrugBank ID: | DB07118 |
| Buried Surface Area: | 44.34 % |
| Polar Surface area: | 46.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -4.60162 | -1.29392 | 48.6379 |
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 | CG | LEU- 160 | 3.77 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 160 | 3.64 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 160 | 4.33 | 0 | Hydrophobic |
| C4A | CD1 | LEU- 300 | 3.76 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 300 | 4.28 | 0 | Hydrophobic |
| O2 | NH1 | ARG- 303 | 2.72 | 139.6 | H-Bond (Protein Donor) |
| C8 | CE | MET- 304 | 3.57 | 0 | Hydrophobic |
