sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2014-01-23
| 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: | 71.087 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | ANP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.046 | 624.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.68 | 44.32 |
| According to VolSite | |
| HET Code: | HFG |
|---|---|
| Formula: | C16H18BrClN3O3 |
| Molecular weight: | 415.689 g/mol |
| DrugBank ID: | DB04866 |
| Buried Surface Area: | 77.15 % |
| 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 |
|---|---|---|
| 19.8589 | 53.4849 | 12.5877 |
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 | 4.29 | 0 | Hydrophobic |
| BR1 | CB | PHE- 335 | 4.06 | 0 | Hydrophobic |
| CL1 | CB | PHE- 335 | 3.77 | 0 | Hydrophobic |
| C6 | CB | PHE- 335 | 3.56 | 0 | Hydrophobic |
| C7 | CB | PHE- 335 | 3.63 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 335 | 3.74 | 0 | Aromatic Face/Face |
| BR1 | CB | GLU- 338 | 3.52 | 0 | Hydrophobic |
| BR1 | CG2 | VAL- 339 | 3.45 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 339 | 4.25 | 0 | Hydrophobic |
| BR1 | CB | PRO- 358 | 3.61 | 0 | Hydrophobic |
| CL1 | CG | PRO- 358 | 3.6 | 0 | Hydrophobic |
| C6 | CG | PRO- 358 | 3.59 | 0 | Hydrophobic |
| C7 | CB | PRO- 358 | 3.44 | 0 | Hydrophobic |
| C3' | CG2 | THR- 359 | 4.28 | 0 | Hydrophobic |
| N1' | OE1 | GLU- 361 | 2.77 | 157.44 | H-Bond (Ligand Donor) |
| N1' | OE2 | GLU- 361 | 3.18 | 124.27 | H-Bond (Ligand Donor) |
| N1' | OE1 | GLU- 361 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N1' | OE2 | GLU- 361 | 3.18 | 0 | Ionic (Ligand Cationic) |
| C8 | CD | ARG- 390 | 3.91 | 0 | Hydrophobic |
| C5' | CH2 | TRP- 407 | 4.26 | 0 | Hydrophobic |
| C39 | CZ3 | TRP- 407 | 4.04 | 0 | Hydrophobic |
| C5' | CB | GLU- 409 | 4.09 | 0 | Hydrophobic |
| C3' | CE2 | PHE- 454 | 3.68 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 454 | 3.77 | 0 | Hydrophobic |
| O7' | NE2 | HIS- 480 | 2.89 | 177.52 | H-Bond (Protein Donor) |
| C5' | CB | SER- 508 | 4.01 | 0 | Hydrophobic |
| O7' | O2A | ANP- 801 | 2.95 | 152.14 | H-Bond (Ligand Donor) |
| C39 | C5' | ANP- 801 | 4.17 | 0 | Hydrophobic |
