sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-09-28
| Name: | ATP-dependent protease Lon |
|---|---|
| ID: | B6YU74_THEON |
| AC: | B6YU74 |
| Organism: | Thermococcus onnurineus |
| Reign: | Archaea |
| TaxID: | 523850 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.513 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.053 | 357.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.28 | 54.72 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.46 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -35.1607 | -61.6197 | -9.14848 |
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 |
| N6 | O | ILE- 44 | 2.78 | 145.88 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 44 | 2.88 | 170.07 | H-Bond (Protein Donor) |
| O3B | N | GLY- 70 | 2.71 | 162.07 | H-Bond (Protein Donor) |
| O1B | N | THR- 71 | 3.19 | 159.17 | H-Bond (Protein Donor) |
| O3A | N | GLY- 72 | 3.31 | 148.51 | H-Bond (Protein Donor) |
| O1B | N | LYS- 73 | 2.98 | 159.7 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 73 | 2.63 | 157.68 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 73 | 2.63 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 73 | 3.8 | 0 | Ionic (Protein Cationic) |
| O2B | N | SER- 74 | 2.95 | 161.3 | H-Bond (Protein Donor) |
| O1A | N | MET- 75 | 2.97 | 146.84 | H-Bond (Protein Donor) |
| C2' | SD | MET- 75 | 3.99 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 338 | 4.31 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 342 | 2.6 | 162.88 | H-Bond (Ligand Donor) |
| C1' | CB | LEU- 378 | 4.27 | 0 | Hydrophobic |
| C5' | CG | ARG- 379 | 3.58 | 0 | Hydrophobic |
| C4' | CB | ARG- 379 | 4.27 | 0 | Hydrophobic |
| N6 | O | HOH- 672 | 2.95 | 154.13 | H-Bond (Ligand Donor) |
| O3B | O | HOH- 772 | 3.05 | 179.98 | H-Bond (Protein Donor) |
| N3 | O | HOH- 830 | 2.84 | 166.19 | H-Bond (Protein Donor) |
