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
2012-10-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.770 | 5.080 | 4.860 | 0.550 | 6.300 | 6 |
| Name: | Sphingosine kinase 1 |
|---|---|
| ID: | SPHK1_HUMAN |
| AC: | Q9NYA1 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.91 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 30.931 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.609 | 864.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.31 | 54.69 |
| According to VolSite | |
| HET Code: | UUL |
|---|---|
| Formula: | C15H11ClN2OS |
| Molecular weight: | 302.779 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 74.55 % |
| Polar Surface area: | 73.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 1.1657 | -33.5583 | -6.22985 |
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 |
| C12 | CG2 | ILE- 174 | 3.79 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 174 | 3.82 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 174 | 3.69 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 177 | 3.53 | 0 | Hydrophobic |
| O20 | OD2 | ASP- 178 | 2.62 | 164 | H-Bond (Ligand Donor) |
| C18 | CB | PHE- 192 | 4.48 | 0 | Hydrophobic |
| N6 | OG1 | THR- 196 | 3.01 | 145.86 | H-Bond (Ligand Donor) |
| S4 | CG2 | THR- 196 | 3.85 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 259 | 4.02 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 261 | 4.02 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 268 | 3.83 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 268 | 4.07 | 0 | Hydrophobic |
| C19 | SD | MET- 272 | 3.63 | 0 | Hydrophobic |
| CL | CE1 | PHE- 288 | 3.38 | 0 | Hydrophobic |
| S4 | CD2 | LEU- 299 | 4.04 | 0 | Hydrophobic |
| C9 | CB | LEU- 302 | 4.4 | 0 | Hydrophobic |
| S4 | CB | PHE- 303 | 3.92 | 0 | Hydrophobic |
| C14 | SD | MET- 306 | 3.91 | 0 | Hydrophobic |
| C7 | CE | MET- 306 | 3.78 | 0 | Hydrophobic |
| CL | CD1 | LEU- 319 | 4.1 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 319 | 4.31 | 0 | Hydrophobic |
