sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2014-04-02
| Name: | Proline--tRNA ligase |
|---|---|
| ID: | SYP_PLAF7 |
| AC: | Q8I5R7 |
| Organism: | Plasmodium falciparum |
| Reign: | Eukaryota |
| TaxID: | 36329 |
| EC Number: | 6.1.1.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.901 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 3 |
| Cofactors: | ANP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.967 | 583.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.27 | 38.73 |
| According to VolSite | |
| HET Code: | HFG |
|---|---|
| Formula: | C16H18BrClN3O3 |
| Molecular weight: | 415.689 g/mol |
| DrugBank ID: | DB04866 |
| Buried Surface Area: | 76.09 % |
| 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 |
|---|---|---|
| -23.5484 | 6.82463 | -32.7292 |
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 |
| CL1 | CD1 | LEU- 325 | 3.93 | 0 | Hydrophobic |
| BR1 | CB | PHE- 335 | 3.84 | 0 | Hydrophobic |
| CL1 | CB | PHE- 335 | 4.21 | 0 | Hydrophobic |
| C6 | CB | PHE- 335 | 3.79 | 0 | Hydrophobic |
| C7 | CB | PHE- 335 | 3.58 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 335 | 3.67 | 0 | Aromatic Face/Face |
| BR1 | CB | GLU- 338 | 3.78 | 0 | Hydrophobic |
| BR1 | CG2 | VAL- 339 | 3.43 | 0 | Hydrophobic |
| BR1 | CB | PRO- 358 | 3.64 | 0 | Hydrophobic |
| CL1 | CG | PRO- 358 | 3.5 | 0 | Hydrophobic |
| C6 | CG | PRO- 358 | 3.48 | 0 | Hydrophobic |
| C7 | CB | PRO- 358 | 3.49 | 0 | Hydrophobic |
| N1' | OG1 | THR- 359 | 3.02 | 120.5 | H-Bond (Ligand Donor) |
| C5 | CG2 | THR- 359 | 3.62 | 0 | Hydrophobic |
| N1' | OE2 | GLU- 361 | 3.38 | 0 | Ionic (Ligand Cationic) |
| N1' | OE1 | GLU- 361 | 2.59 | 0 | Ionic (Ligand Cationic) |
| N1' | OE1 | GLU- 361 | 2.59 | 156.01 | H-Bond (Ligand Donor) |
| O4' | NH2 | ARG- 390 | 3.31 | 120.58 | H-Bond (Protein Donor) |
| C8 | CD | ARG- 390 | 4.25 | 0 | Hydrophobic |
| C5' | CH2 | TRP- 407 | 4.05 | 0 | Hydrophobic |
| C4' | CZ3 | TRP- 407 | 3.93 | 0 | Hydrophobic |
| C5' | CB | GLU- 409 | 4.13 | 0 | Hydrophobic |
| C3' | CZ | PHE- 454 | 3.77 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 454 | 3.6 | 0 | Hydrophobic |
| O7' | OG1 | THR- 478 | 2.88 | 152.95 | H-Bond (Protein Donor) |
| O7' | NE2 | HIS- 480 | 2.63 | 168.88 | H-Bond (Protein Donor) |
| C5' | CB | SER- 508 | 4.4 | 0 | Hydrophobic |
| C39 | C5' | ANP- 802 | 4.29 | 0 | Hydrophobic |
