sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-01-11
| 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: | 59.569 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.139 | 1444.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.63 | 55.37 |
| According to VolSite | |
| HET Code: | XNN |
|---|---|
| Formula: | C22H27N8S |
| Molecular weight: | 435.568 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.86 % |
| Polar Surface area: | 120.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -5.45448 | -1.91784 | 19.317 |
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 |
| N29 | OD2 | ASP- 27 | 3.14 | 143.12 | H-Bond (Ligand Donor) |
| N29 | OD1 | ASP- 27 | 3.06 | 145.91 | H-Bond (Ligand Donor) |
| N29 | OD2 | ASP- 27 | 3.14 | 0 | Ionic (Ligand Cationic) |
| N29 | OD1 | ASP- 27 | 3.06 | 0 | Ionic (Ligand Cationic) |
| C01 | CB | ALA- 224 | 3.79 | 0 | Hydrophobic |
| C04 | CB | ALA- 224 | 3.42 | 0 | Hydrophobic |
| C26 | CB | ALA- 226 | 4.28 | 0 | Hydrophobic |
| C31 | CB | ALA- 226 | 3.72 | 0 | Hydrophobic |
| C23 | CB | GLU- 227 | 3.53 | 0 | Hydrophobic |
| C22 | CB | GLU- 227 | 4 | 0 | Hydrophobic |
| C01 | CB | ALA- 230 | 3.69 | 0 | Hydrophobic |
| C24 | CB | PRO- 246 | 4.15 | 0 | Hydrophobic |
| C22 | CB | PRO- 246 | 3.72 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 250 | 3.49 | 0 | Hydrophobic |
| C26 | CG2 | THR- 253 | 4.46 | 0 | Hydrophobic |
| C07 | CB | ALA- 256 | 3.51 | 0 | Hydrophobic |
| C01 | CE1 | PHE- 260 | 4.12 | 0 | Hydrophobic |
| S02 | CD1 | PHE- 260 | 4.06 | 0 | Hydrophobic |
| C04 | CB | PHE- 260 | 3.51 | 0 | Hydrophobic |
| C01 | SG | CYS- 282 | 3.56 | 0 | Hydrophobic |
| C08 | CB | ALA- 285 | 4.1 | 0 | Hydrophobic |
| C03 | CB | ALA- 285 | 3.84 | 0 | Hydrophobic |
