sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2008-07-01
| Name: | Dodecin |
|---|---|
| ID: | DODEC_HALHL |
| AC: | A1WUH0 |
| Organism: | Halorhodospira halophila |
| Reign: | Bacteria |
| TaxID: | 349124 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 27 % |
| K | 36 % |
| L | 36 % |
| B-Factor: | 35.386 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.375 | 972.000 |
| % Hydrophobic | % Polar |
|---|---|
| 38.19 | 61.81 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 55.87 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -26.8247 | -11.7293 | 19.9889 |
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 |
| C8M | CE1 | TYR- 6 | 4 | 0 | Hydrophobic |
| C7M | CG2 | THR- 12 | 4.46 | 0 | Hydrophobic |
| C4' | CD | ARG- 38 | 3.96 | 0 | Hydrophobic |
| C2' | CB | ARG- 38 | 3.95 | 0 | Hydrophobic |
| C7M | CZ2 | TRP- 39 | 3.55 | 0 | Hydrophobic |
| C8M | CH2 | TRP- 39 | 4.06 | 0 | Hydrophobic |
| C9A | CB | TRP- 39 | 4.47 | 0 | Hydrophobic |
| C2' | CE3 | TRP- 39 | 4.06 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 39 | 3.54 | 0 | Aromatic Face/Face |
| O4 | NE | ARG- 46 | 2.76 | 140.63 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 46 | 3.17 | 125.89 | H-Bond (Protein Donor) |
| N5 | NH2 | ARG- 46 | 2.98 | 145.42 | H-Bond (Protein Donor) |
| C7M | CD | ARG- 46 | 3.79 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 58 | 2.98 | 164.16 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 58 | 2.73 | 172.6 | H-Bond (Ligand Donor) |
| C7M | CB | GLN- 58 | 4.42 | 0 | Hydrophobic |
| C8M | CG | GLN- 58 | 3.55 | 0 | Hydrophobic |
| C7M | CG2 | THR- 60 | 4.23 | 0 | Hydrophobic |
