sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2005-01-05
| 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: | 28.897 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.721 | 1782.000 |
| % Hydrophobic | % Polar |
|---|---|
| 47.92 | 52.08 |
| According to VolSite | |
| HET Code: | RRC |
|---|---|
| Formula: | C19H26N6O |
| Molecular weight: | 354.449 g/mol |
| DrugBank ID: | DB06195 |
| Buried Surface Area: | 54.9 % |
| Polar Surface area: | 87.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -9.48742 | 45.5597 | 11.6001 |
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 |
| NAO | OG | SER- 12 | 2.61 | 152.42 | H-Bond (Protein Donor) |
| CAD | CB | SER- 12 | 3.64 | 0 | Hydrophobic |
| CBA | CG2 | VAL- 19 | 3.71 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 41 | 3.89 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 41 | 3.6 | 0 | Hydrophobic |
| NAS | OG1 | THR- 47 | 3.18 | 131.47 | H-Bond (Ligand Donor) |
| NAL | N | THR- 47 | 3.39 | 165.55 | H-Bond (Protein Donor) |
| CAB | CG2 | THR- 47 | 4.14 | 0 | Hydrophobic |
| CAI | CZ | TYR- 84 | 3.99 | 0 | Hydrophobic |
| CAG | CE2 | TYR- 84 | 3.39 | 0 | Hydrophobic |
| CAY | CB | TYR- 84 | 3.33 | 0 | Hydrophobic |
| CAF | CD | ARG- 86 | 3.3 | 0 | Hydrophobic |
| CAY | CG1 | VAL- 115 | 3.76 | 0 | Hydrophobic |
| CAK | CD2 | TYR- 127 | 4.45 | 0 | Hydrophobic |
| CAI | CG | TYR- 127 | 4.34 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 231 | 4.13 | 0 | Hydrophobic |
