sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2013-05-30
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 44.386 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.002 | 1174.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.68 | 56.32 |
| According to VolSite | |
| HET Code: | 1V2 |
|---|---|
| Formula: | C23H26Cl2N3O2S |
| Molecular weight: | 479.442 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.42 % |
| Polar Surface area: | 98.06 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 29.9065 | 81.7137 | 0.691129 |
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 |
| O2 | OD2 | ASP- 81 | 2.71 | 166.83 | H-Bond (Ligand Donor) |
| C19 | CD2 | LEU- 167 | 4.02 | 0 | Hydrophobic |
| C23 | CB | SER- 168 | 4.36 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 174 | 4.07 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 174 | 4.42 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 174 | 4.25 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 174 | 4.03 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 174 | 4 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 174 | 3.87 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 177 | 3.61 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 178 | 3.08 | 150.04 | H-Bond (Ligand Donor) |
| O1 | OD2 | ASP- 178 | 2.65 | 132.75 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 178 | 3.08 | 0 | Ionic (Ligand Cationic) |
| N2 | OD2 | ASP- 178 | 3.52 | 0 | Ionic (Ligand Cationic) |
| C7 | CD1 | PHE- 192 | 3.68 | 0 | Hydrophobic |
| C21 | CZ | PHE- 192 | 3.61 | 0 | Hydrophobic |
| C5 | CB | PHE- 192 | 4.05 | 0 | Hydrophobic |
| S1 | CG2 | THR- 196 | 3.66 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 259 | 4.06 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 261 | 3.54 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 268 | 4.21 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 268 | 3.85 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 268 | 3.61 | 0 | Hydrophobic |
| C7 | CE | MET- 272 | 4.17 | 0 | Hydrophobic |
| C4 | SD | MET- 272 | 3.47 | 0 | Hydrophobic |
| CL1 | CB | ALA- 274 | 4.13 | 0 | Hydrophobic |
| CL1 | CG | PHE- 288 | 4.35 | 0 | Hydrophobic |
| CL2 | CD1 | PHE- 288 | 3.41 | 0 | Hydrophobic |
| C17 | CB | LEU- 302 | 3.9 | 0 | Hydrophobic |
| S1 | CB | PHE- 303 | 3.55 | 0 | Hydrophobic |
| S1 | CD1 | PHE- 303 | 3.47 | 0 | Hydrophobic |
| CL1 | SD | MET- 306 | 4.41 | 0 | Hydrophobic |
| C13 | SD | MET- 306 | 3.58 | 0 | Hydrophobic |
| CL2 | CD1 | LEU- 319 | 3.55 | 0 | Hydrophobic |
| O1 | O | HOH- 516 | 2.69 | 179.98 | H-Bond (Protein Donor) |
