sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2005-08-22
| Name: | Lipoate-protein ligase A subunit 1 |
|---|---|
| ID: | LPLAN_THEAC |
| AC: | Q9HKT1 |
| Organism: | Thermoplasma acidophilum |
| Reign: | Archaea |
| TaxID: | 273075 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.507 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.590 | 1123.875 |
| % Hydrophobic | % Polar |
|---|---|
| 57.36 | 42.64 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 71.27 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 10.0569 | 27.8628 | 27.6265 |
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 |
| O3G | CZ | ARG- 72 | 2.91 | 0 | Ionic (Protein Cationic) |
| O3' | O | ALA- 78 | 3.39 | 129.97 | H-Bond (Ligand Donor) |
| C3' | CG1 | VAL- 79 | 4.26 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 79 | 4.37 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 79 | 3.22 | 0 | Hydrophobic |
| N7 | N | TYR- 80 | 3.14 | 163.62 | H-Bond (Protein Donor) |
| N6 | O | TYR- 80 | 2.81 | 175.51 | H-Bond (Ligand Donor) |
| O1B | NZ | LYS- 145 | 2.64 | 155.46 | H-Bond (Protein Donor) |
| O4' | NZ | LYS- 145 | 2.62 | 152.55 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 145 | 2.64 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 145 | 3.43 | 0 | Ionic (Protein Cationic) |
| C1' | CD | LYS- 145 | 4.13 | 0 | Hydrophobic |
| C2' | CD1 | LEU- 173 | 4.18 | 0 | Hydrophobic |
| C3' | CD2 | LEU- 177 | 3.79 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 196 | 4.33 | 0 | Hydrophobic |
| O2B | MG | MG- 1301 | 2.46 | 0 | Metal Acceptor |
