sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2015-01-14
| Name: | Pyridoxal kinase, putative |
|---|---|
| ID: | C4LVZ4_ENTHI |
| AC: | C4LVZ4 |
| Organism: | Entamoeba histolytica |
| Reign: | Eukaryota |
| TaxID: | 5759 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 26.478 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.108 | 816.750 |
| % Hydrophobic | % Polar |
|---|---|
| 53.72 | 46.28 |
| According to VolSite | |
| HET Code: | PLP |
|---|---|
| Formula: | C8H8NO6P |
| Molecular weight: | 245.126 g/mol |
| DrugBank ID: | DB00114 |
| Buried Surface Area: | 63.41 % |
| Polar Surface area: | 132.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 30.8422 | -39.1479 | -11.7457 |
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 |
| C2A | CB | SER- 10 | 3.79 | 0 | Hydrophobic |
| C3 | CB | SER- 10 | 4.31 | 0 | Hydrophobic |
| C2A | CG1 | VAL- 12 | 4.16 | 0 | Hydrophobic |
| C2A | CG2 | VAL- 17 | 4.19 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 17 | 3.54 | 0 | Hydrophobic |
| C4 | CB | VAL- 17 | 3.88 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 17 | 4.29 | 0 | Hydrophobic |
| C2A | CD1 | LEU- 41 | 3.59 | 0 | Hydrophobic |
| N1 | N | THR- 45 | 3.35 | 159.31 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 45 | 3.29 | 143.36 | H-Bond (Protein Donor) |
| C2A | CG2 | THR- 45 | 4.44 | 0 | Hydrophobic |
| C2A | CZ | TYR- 83 | 4.07 | 0 | Hydrophobic |
| C3 | CB | TYR- 83 | 4.46 | 0 | Hydrophobic |
| C5A | CE1 | TYR- 121 | 3.78 | 0 | Hydrophobic |
