sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2004-05-30
| Name: | Isoleucine--tRNA ligase |
|---|---|
| ID: | SYI_THET8 |
| AC: | P56690 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | 6.1.1.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 39.574 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.295 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 32.38 | 67.62 |
| According to VolSite | |
| HET Code: | VMS |
|---|---|
| Formula: | C15H23N7O7S |
| Molecular weight: | 445.451 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.59 % |
| 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: | 7 |
| X | Y | Z |
|---|---|---|
| 75.3413 | 20.7348 | 22.9527 |
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 |
| O2' | NE1 | TRP- 227 | 2.99 | 130.06 | H-Bond (Protein Donor) |
| C5' | CB | THR- 228 | 4.49 | 0 | Hydrophobic |
| OBC | N | THR- 229 | 3.3 | 145.1 | H-Bond (Protein Donor) |
| OBC | OG1 | THR- 229 | 2.96 | 149.56 | H-Bond (Protein Donor) |
| C5' | CG2 | THR- 229 | 3.92 | 0 | Hydrophobic |
| OBC | OG1 | THR- 230 | 2.79 | 161.74 | H-Bond (Protein Donor) |
| CG2 | CB | THR- 233 | 4.18 | 0 | Hydrophobic |
| N6 | O | TYR- 308 | 2.76 | 141.89 | H-Bond (Ligand Donor) |
| N | O | HIS- 319 | 2.91 | 137.39 | H-Bond (Ligand Donor) |
| CG2 | CB | ALA- 321 | 4.01 | 0 | Hydrophobic |
| CG1 | CB | ALA- 321 | 4.38 | 0 | Hydrophobic |
| CG1 | CB | PHE- 324 | 3.87 | 0 | Hydrophobic |
| N | OD1 | ASP- 328 | 2.84 | 162.49 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 328 | 2.84 | 0 | Ionic (Ligand Cationic) |
| N | OD2 | ASP- 328 | 3.5 | 0 | Ionic (Ligand Cationic) |
| OAZ | O | HOH- 1008 | 3.26 | 127.45 | H-Bond (Protein Donor) |
