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
2006-08-24
| Name: | Pyridoxine kinase |
|---|---|
| ID: | PDXK_BACSU |
| AC: | P39610 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 100 % |
| B-Factor: | 34.058 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.982 | 860.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.14 | 56.86 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.97 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -0.306444 | -1.69915 | -42.4806 |
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 |
| O1B | ND2 | ASN- 141 | 3.06 | 156.83 | H-Bond (Protein Donor) |
| O3B | ND2 | ASN- 141 | 3.05 | 125.82 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 178 | 2.88 | 158.16 | H-Bond (Protein Donor) |
| C3' | CB | THR- 178 | 4.11 | 0 | Hydrophobic |
| N7 | N | GLY- 181 | 3.06 | 166.37 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 182 | 3.91 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 182 | 3.75 | 0 | Ionic (Protein Cationic) |
| O3' | OD2 | ASP- 190 | 2.64 | 169.05 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 190 | 2.89 | 150.02 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 190 | 2.78 | 141.33 | H-Bond (Ligand Donor) |
| N6 | O | ILE- 206 | 2.98 | 163.86 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 206 | 3.07 | 170.47 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 214 | 3.77 | 0 | Hydrophobic |
| O2B | N | GLY- 215 | 2.87 | 139.57 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 218 | 4.18 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 243 | 4.1 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 243 | 3.66 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 247 | 3.78 | 0 | Hydrophobic |
