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
2011-01-07
| Name: | Ketohexokinase |
|---|---|
| ID: | KHK_HUMAN |
| AC: | P50053 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 47.478 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.047 | 1049.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.41 | 56.59 |
| According to VolSite | |
| HET Code: | XNB |
|---|---|
| Formula: | C21H27N8S |
| Molecular weight: | 423.558 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.6 % |
| Polar Surface area: | 120.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -5.1232 | -1.89433 | 19.368 |
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 |
| N28 | OD1 | ASP- 27 | 2.76 | 134.2 | H-Bond (Ligand Donor) |
| N28 | OD1 | ASP- 27 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N28 | OD2 | ASP- 27 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C01 | CB | ALA- 224 | 3.87 | 0 | Hydrophobic |
| C04 | CB | ALA- 224 | 3.45 | 0 | Hydrophobic |
| C26 | CB | ALA- 226 | 3.95 | 0 | Hydrophobic |
| C23 | CB | GLU- 227 | 3.41 | 0 | Hydrophobic |
| C22 | CB | GLU- 227 | 4.25 | 0 | Hydrophobic |
| C01 | CB | ALA- 230 | 3.73 | 0 | Hydrophobic |
| C22 | CB | PRO- 246 | 3.67 | 0 | Hydrophobic |
| C21 | CB | VAL- 250 | 4.32 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 250 | 4.4 | 0 | Hydrophobic |
| C26 | CG2 | THR- 253 | 4.46 | 0 | Hydrophobic |
| C30 | CG2 | THR- 253 | 4.18 | 0 | Hydrophobic |
| C07 | CB | ALA- 256 | 3.68 | 0 | Hydrophobic |
| S02 | CD1 | PHE- 260 | 4.01 | 0 | Hydrophobic |
| C04 | CB | PHE- 260 | 3.41 | 0 | Hydrophobic |
| C01 | SG | CYS- 282 | 3.3 | 0 | Hydrophobic |
| S02 | CB | ALA- 285 | 3.88 | 0 | Hydrophobic |
