sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2016-05-17
| Name: | Methionine--tRNA ligase |
|---|---|
| ID: | SYM_BRUSU |
| AC: | P59078 |
| Organism: | Brucella suis biovar 1 |
| Reign: | Bacteria |
| TaxID: | 204722 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 49.584 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.945 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | 415 |
|---|---|
| Formula: | C18H23ClN3O2 |
| Molecular weight: | 348.847 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.52 % |
| Polar Surface area: | 66.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -7.33888 | 16.2744 | 67.1501 |
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 |
| CLC | CB | ALA- 11 | 3.76 | 0 | Hydrophobic |
| CLC | CG1 | ILE- 12 | 3.76 | 0 | Hydrophobic |
| NAP | OD2 | ASP- 51 | 3.76 | 0 | Ionic (Ligand Cationic) |
| NAQ | OD2 | ASP- 51 | 2.96 | 146.1 | H-Bond (Ligand Donor) |
| NAR | OD1 | ASP- 51 | 3.43 | 155.5 | H-Bond (Ligand Donor) |
| NAR | OD2 | ASP- 51 | 2.95 | 147.69 | H-Bond (Ligand Donor) |
| CAE | CB | HIS- 53 | 3.53 | 0 | Hydrophobic |
| CAK | CG2 | VAL- 229 | 4.31 | 0 | Hydrophobic |
| CAG | CB | VAL- 229 | 3.75 | 0 | Hydrophobic |
| CAH | CB | VAL- 229 | 3.74 | 0 | Hydrophobic |
| CAA | CE3 | TRP- 230 | 3.61 | 0 | Hydrophobic |
| CAE | CB | ASP- 232 | 4.32 | 0 | Hydrophobic |
| CAX | CB | ALA- 233 | 3.39 | 0 | Hydrophobic |
| CAA | CG | LEU- 234 | 3.6 | 0 | Hydrophobic |
| CAJ | CD2 | LEU- 234 | 4.07 | 0 | Hydrophobic |
| CLC | CZ | TYR- 237 | 3.8 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 265 | 3.8 | 0 | Hydrophobic |
| CAA | CB | PHE- 268 | 3.31 | 0 | Hydrophobic |
