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
2003-11-10
| Name: | Pyridoxal kinase |
|---|---|
| ID: | PDXK_SHEEP |
| AC: | P82197 |
| Organism: | Ovis aries |
| Reign: | Eukaryota |
| TaxID: | 9940 |
| EC Number: | 2.7.1.35 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 100 % |
| B-Factor: | 26.695 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ADP |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.405 | 266.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.96 | 43.04 |
| According to VolSite | |
| HET Code: | PLP |
|---|---|
| Formula: | C8H8NO6P |
| Molecular weight: | 245.126 g/mol |
| DrugBank ID: | DB00114 |
| Buried Surface Area: | 77.46 % |
| 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 |
|---|---|---|
| 43.0391 | 23.3213 | -17.3875 |
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 |
| N1 | OG | SER- 12 | 2.75 | 170.48 | H-Bond (Protein Donor) |
| C2A | CB | SER- 12 | 3.81 | 0 | Hydrophobic |
| C2A | CG1 | VAL- 14 | 4.37 | 0 | Hydrophobic |
| C2A | CG1 | VAL- 19 | 4.11 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 19 | 4.41 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 19 | 4.15 | 0 | Hydrophobic |
| C2A | CD2 | PHE- 43 | 4.07 | 0 | Hydrophobic |
| C3 | CB | HIS- 46 | 4.1 | 0 | Hydrophobic |
| O3 | N | THR- 47 | 3.32 | 145.9 | H-Bond (Protein Donor) |
| C2A | CE2 | TYR- 84 | 3.78 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 84 | 3.96 | 0 | Aromatic Face/Face |
| C5A | CG1 | VAL- 115 | 4.38 | 0 | Hydrophobic |
| C4A | CZ | TYR- 127 | 3.73 | 0 | Hydrophobic |
| C5A | CG1 | VAL- 231 | 4.36 | 0 | Hydrophobic |
| C4A | CG1 | VAL- 231 | 3.4 | 0 | Hydrophobic |
| O4P | N | GLY- 232 | 3.44 | 130.15 | H-Bond (Protein Donor) |
| O2P | N | GLY- 232 | 2.93 | 168.37 | H-Bond (Protein Donor) |
| O3P | N | GLY- 232 | 3.3 | 122.41 | H-Bond (Protein Donor) |
| O3P | N | ASP- 235 | 3.11 | 156.35 | H-Bond (Protein Donor) |
| O1P | ZN | ZN- 3403 | 2.45 | 0 | Metal Acceptor |
