sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.620 Å
X-ray
2013-04-18
| Name: | Bifunctional glutamate/proline--tRNA ligase |
|---|---|
| ID: | SYEP_HUMAN |
| AC: | P07814 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 6.1.1.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 65.105 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.809 | 1269.000 |
| % Hydrophobic | % Polar |
|---|---|
| 38.30 | 61.70 |
| According to VolSite | |
| HET Code: | HFG |
|---|---|
| Formula: | C16H18BrClN3O3 |
| Molecular weight: | 415.689 g/mol |
| DrugBank ID: | DB04866 |
| Buried Surface Area: | 62.41 % |
| Polar Surface area: | 86.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -27.1143 | 14.5299 | -10.6148 |
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 |
| BR1 | CB | PHE- 97 | 3.5 | 0 | Hydrophobic |
| CL1 | CB | PHE- 97 | 4.44 | 0 | Hydrophobic |
| C6 | CB | PHE- 97 | 3.74 | 0 | Hydrophobic |
| C7 | CB | PHE- 97 | 3.25 | 0 | Hydrophobic |
| BR1 | CB | GLU- 100 | 3.9 | 0 | Hydrophobic |
| BR1 | CG1 | VAL- 101 | 3.4 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 101 | 3.84 | 0 | Hydrophobic |
| BR1 | CB | PRO- 120 | 3.89 | 0 | Hydrophobic |
| CL1 | CG | PRO- 120 | 3.41 | 0 | Hydrophobic |
| C6 | CG | PRO- 120 | 3.72 | 0 | Hydrophobic |
| C7 | CB | PRO- 120 | 3.71 | 0 | Hydrophobic |
| N1' | OG1 | THR- 121 | 2.73 | 145.18 | H-Bond (Ligand Donor) |
| C5 | CG2 | THR- 121 | 3.99 | 0 | Hydrophobic |
| N1' | OE2 | GLU- 123 | 3.46 | 0 | Ionic (Ligand Cationic) |
| N1' | OE1 | GLU- 123 | 3.85 | 0 | Ionic (Ligand Cationic) |
| O4' | NH2 | ARG- 152 | 3.13 | 121.15 | H-Bond (Protein Donor) |
| C8 | CD | ARG- 152 | 4.06 | 0 | Hydrophobic |
| C5' | CH2 | TRP- 169 | 4.18 | 0 | Hydrophobic |
| C5' | CB | GLU- 171 | 4.38 | 0 | Hydrophobic |
| C3' | CZ | PHE- 216 | 3.57 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 216 | 3.81 | 0 | Hydrophobic |
| O7' | NE2 | HIS- 242 | 2.68 | 165.22 | H-Bond (Ligand Donor) |
| C4' | CB | SER- 272 | 3.98 | 0 | Hydrophobic |
