sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-11-02
| Name: | Hygromycin-B 4-O-kinase |
|---|---|
| ID: | KHYB_ECOLX |
| AC: | P00557 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | 2.7.1.163 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 33.239 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.260 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 64.84 | 35.16 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 35.09 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 22.3439 | -8.90045 | -4.31271 |
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 |
| C1' | CD1 | LEU- 28 | 4.43 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 28 | 3.64 | 0 | Hydrophobic |
| O1A | OG | SER- 29 | 2.86 | 166.63 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 36 | 3.66 | 0 | Hydrophobic |
| N6 | O | ARG- 93 | 3.3 | 136.34 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 95 | 2.84 | 156.52 | H-Bond (Protein Donor) |
