sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.590 Å
X-ray
2007-05-22
| Name: | Dodecin |
|---|---|
| ID: | DODEC_THET8 |
| AC: | Q5SIE3 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 4 % |
| F | 36 % |
| J | 36 % |
| K | 25 % |
| B-Factor: | 34.281 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.284 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.47 | 60.53 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 58.27 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 3.56484 | -0.602323 | -31.0194 |
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 |
| O2P | NZ | LYS- 3 | 3.12 | 167.92 | H-Bond (Protein Donor) |
| O2P | NZ | LYS- 3 | 3.12 | 0 | Ionic (Protein Cationic) |
| C8M | CD2 | TYR- 5 | 4.27 | 0 | Hydrophobic |
| C5' | CZ | TYR- 5 | 4.07 | 0 | Hydrophobic |
| C7M | CG1 | VAL- 11 | 3.99 | 0 | Hydrophobic |
| C8M | CG1 | VAL- 11 | 3.73 | 0 | Hydrophobic |
| C2' | CB | ASP- 37 | 4.46 | 0 | Hydrophobic |
| C7M | CZ2 | TRP- 38 | 4.39 | 0 | Hydrophobic |
| C8M | CH2 | TRP- 38 | 4.11 | 0 | Hydrophobic |
| C2' | CE3 | TRP- 38 | 4.27 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 38 | 3.91 | 0 | Aromatic Face/Face |
| O2 | NE2 | GLN- 57 | 2.72 | 149.33 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 57 | 2.55 | 162.24 | H-Bond (Ligand Donor) |
| C7M | CB | GLN- 57 | 4.43 | 0 | Hydrophobic |
| C8M | CG | GLN- 57 | 3.96 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 59 | 3.94 | 0 | Hydrophobic |
