sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-08-22
| Name: | Proline--tRNA ligase |
|---|---|
| ID: | SYP_RHOPA |
| AC: | Q6N5P6 |
| Organism: | Rhodopseudomonas palustris |
| Reign: | Bacteria |
| TaxID: | 258594 |
| EC Number: | 6.1.1.15 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 36.658 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.287 | 2430.000 |
| % Hydrophobic | % Polar |
|---|---|
| 33.06 | 66.94 |
| According to VolSite | |
| HET Code: | PSD |
|---|---|
| Formula: | C15H22N7O7P |
| Molecular weight: | 443.352 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.57 % |
| Polar Surface area: | 224.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 33.3715 | 77.6602 | 19.2266 |
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 |
| N | OG1 | THR- 109 | 2.8 | 133.61 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 111 | 2.87 | 158.18 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 111 | 2.87 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 111 | 3.69 | 0 | Ionic (Ligand Cationic) |
| O1P | NH2 | ARG- 140 | 2.93 | 153.13 | H-Bond (Protein Donor) |
| O1P | NH1 | ARG- 140 | 3.24 | 137.66 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 140 | 3.53 | 0 | Ionic (Protein Cationic) |
| DuAr | DuAr | PHE- 155 | 3.82 | 0 | Aromatic Face/Face |
| CG | SD | MET- 157 | 3.54 | 0 | Hydrophobic |
| C1' | CE | MET- 157 | 4 | 0 | Hydrophobic |
| C5' | CE | MET- 157 | 3.84 | 0 | Hydrophobic |
| O2' | O | GLU- 282 | 2.74 | 166.92 | H-Bond (Ligand Donor) |
| C5' | CB | GLN- 285 | 4.19 | 0 | Hydrophobic |
| CB | CE1 | PHE- 287 | 3.52 | 0 | Hydrophobic |
| CB | CB | SER- 315 | 4.18 | 0 | Hydrophobic |
| C2' | CD | ARG- 322 | 4.36 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 322 | 3.92 | 23.36 | Pi/Cation |
