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
2005-01-09
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 26.985 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.981 | 1643.625 |
| % Hydrophobic | % Polar |
|---|---|
| 49.49 | 50.51 |
| According to VolSite | |
| HET Code: | R6C |
|---|---|
| Formula: | C19H25N5O2 |
| Molecular weight: | 355.434 g/mol |
| DrugBank ID: | DB04770 |
| Buried Surface Area: | 55.97 % |
| Polar Surface area: | 85.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 16.7178 | 58.303 | 1.86362 |
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 |
| CAD | CB | SER- 12 | 3.86 | 0 | Hydrophobic |
| CBA | CG2 | VAL- 19 | 3.51 | 0 | Hydrophobic |
| CAH | CG1 | VAL- 41 | 4.1 | 0 | Hydrophobic |
| CAB | CG2 | VAL- 41 | 4.34 | 0 | Hydrophobic |
| CAE | CG2 | VAL- 41 | 3.79 | 0 | Hydrophobic |
| NAS | OG1 | THR- 47 | 3.1 | 141.14 | H-Bond (Ligand Donor) |
| NAL | N | THR- 47 | 3.44 | 162.01 | H-Bond (Protein Donor) |
| CAB | CG2 | THR- 47 | 4.36 | 0 | Hydrophobic |
| CAI | CZ | TYR- 84 | 4.03 | 0 | Hydrophobic |
| CAZ | CD2 | TYR- 84 | 4.35 | 0 | Hydrophobic |
| CAY | CB | TYR- 84 | 3.37 | 0 | Hydrophobic |
| CAF | CD | ARG- 86 | 3.34 | 0 | Hydrophobic |
| CAY | CG1 | VAL- 115 | 3.74 | 0 | Hydrophobic |
| CAK | CE2 | TYR- 127 | 4.31 | 0 | Hydrophobic |
| CAI | CG | TYR- 127 | 4.1 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 231 | 4.3 | 0 | Hydrophobic |
