sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.070 Å
X-ray
2013-01-10
| Name: | Leucyl-tRNA synthetase |
|---|---|
| ID: | Q6KHA5_MYCMO |
| AC: | Q6KHA5 |
| Organism: | Mycoplasma mobile |
| Reign: | Bacteria |
| TaxID: | 267748 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.014 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.085 | 1184.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.89 | 60.11 |
| According to VolSite | |
| HET Code: | LSS |
|---|---|
| Formula: | C16H25N7O7S |
| Molecular weight: | 459.477 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 82.28 % |
| Polar Surface area: | 229.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -28.2432 | 7.99926 | 78.4872 |
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 |
| C9 | CB | MET- 43 | 3.86 | 0 | Hydrophobic |
| C10 | CG | MET- 43 | 3.73 | 0 | Hydrophobic |
| C23 | CB | MET- 43 | 4.13 | 0 | Hydrophobic |
| N4 | O | PHE- 44 | 2.67 | 153.11 | H-Bond (Ligand Donor) |
| C7 | CE1 | PHE- 44 | 3.92 | 0 | Hydrophobic |
| C10 | CD1 | PHE- 44 | 3.9 | 0 | Hydrophobic |
| C25 | CB | PRO- 45 | 4.47 | 0 | Hydrophobic |
| O2A | N | TYR- 46 | 3.2 | 145.78 | H-Bond (Protein Donor) |
| C24 | CE1 | TYR- 60 | 4.38 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 84 | 2.78 | 149.96 | H-Bond (Ligand Donor) |
| N4 | OD2 | ASP- 84 | 2.78 | 0 | Ionic (Ligand Cationic) |
| C11 | CZ3 | TRP- 321 | 3.85 | 0 | Hydrophobic |
| C11 | CB | SER- 324 | 3.92 | 0 | Hydrophobic |
| C10 | CE1 | TYR- 327 | 4.01 | 0 | Hydrophobic |
| O3 | N | GLY- 364 | 3.23 | 144.83 | H-Bond (Protein Donor) |
| O2 | OE2 | GLU- 366 | 2.64 | 170.24 | H-Bond (Ligand Donor) |
| O1 | NE2 | HIS- 367 | 2.84 | 163.29 | H-Bond (Protein Donor) |
| C11 | CB | HIS- 371 | 3.66 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 400 | 3.02 | 135.69 | H-Bond (Protein Donor) |
| N3 | NE2 | GLN- 400 | 3.14 | 152.45 | H-Bond (Protein Donor) |
| N1 | N | ILE- 403 | 3.02 | 168.51 | H-Bond (Protein Donor) |
| N6 | O | ILE- 403 | 3.04 | 166.76 | H-Bond (Ligand Donor) |
| N6 | O | MET- 411 | 3.1 | 151.7 | H-Bond (Ligand Donor) |
| N7 | O | HOH- 2087 | 2.91 | 161.26 | H-Bond (Protein Donor) |
| N3 | O | HOH- 2090 | 2.93 | 131.22 | H-Bond (Protein Donor) |
