sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2008-07-29
| Name: | Dodecin |
|---|---|
| ID: | DODEC_THET8 |
| AC: | Q5SIE3 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 43 % |
| C | 21 % |
| F | 36 % |
| B-Factor: | 19.729 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.149 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.10 | 54.90 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 62.4 % |
| 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 |
|---|---|---|
| 44.6472 | 14.268 | 68.0093 |
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- 5 | 4.02 | 0 | Hydrophobic |
| O5' | OH | TYR- 5 | 3.15 | 152.57 | H-Bond (Protein Donor) |
| O1P | OH | TYR- 5 | 2.69 | 132.94 | H-Bond (Protein Donor) |
| C7M | CG1 | VAL- 11 | 3.67 | 0 | Hydrophobic |
| C8M | CG1 | VAL- 11 | 3.77 | 0 | Hydrophobic |
| O3P | OD2 | ASP- 37 | 2.54 | 159.6 | H-Bond (Protein Donor) |
| C2' | CB | ASP- 37 | 4.31 | 0 | Hydrophobic |
| C7M | CZ | PHE- 38 | 4.24 | 0 | Hydrophobic |
| C8M | CE1 | PHE- 38 | 4.28 | 0 | Hydrophobic |
| C2' | CD1 | PHE- 38 | 4.13 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 38 | 3.96 | 0 | Aromatic Face/Face |
| O4 | NH2 | ARG- 45 | 3.36 | 129.86 | H-Bond (Protein Donor) |
| O4 | NE | ARG- 45 | 2.81 | 153.98 | H-Bond (Protein Donor) |
| N5 | NH2 | ARG- 45 | 3.23 | 154.08 | H-Bond (Protein Donor) |
| C7M | CD | ARG- 45 | 3.92 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 57 | 2.9 | 168.59 | H-Bond (Protein Donor) |
| N3 | OE1 | GLN- 57 | 2.77 | 163.12 | H-Bond (Ligand Donor) |
| C8M | CG | GLN- 57 | 4.19 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 59 | 4.01 | 0 | Hydrophobic |
| O3P | CZ | ARG- 65 | 3.97 | 0 | Ionic (Protein Cationic) |
| O3P | NH1 | ARG- 65 | 2.96 | 159.3 | H-Bond (Protein Donor) |
