sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2012-08-03
| Name: | Tyrosine-protein kinase SYK |
|---|---|
| ID: | KSYK_HUMAN |
| AC: | P43405 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.835 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.168 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 60.47 | 39.53 |
| According to VolSite | |
| HET Code: | 0XF |
|---|---|
| Formula: | C18H26N7O |
| Molecular weight: | 356.445 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.51 % |
| Polar Surface area: | 133.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 1.46885 | 0.978808 | 14.1014 |
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 | CB | LEU- 377 | 4.37 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 377 | 4.46 | 0 | Hydrophobic |
| C22 | CZ | PHE- 382 | 4.16 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 385 | 4.18 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 385 | 4.07 | 0 | Hydrophobic |
| C6 | CB | ALA- 400 | 4.45 | 0 | Hydrophobic |
| N11 | O | GLU- 449 | 2.97 | 171.52 | H-Bond (Ligand Donor) |
| C15 | SD | MET- 450 | 4.04 | 0 | Hydrophobic |
| O10 | N | ALA- 451 | 2.98 | 175.96 | H-Bond (Protein Donor) |
| C26 | CG | PRO- 455 | 4.22 | 0 | Hydrophobic |
| C19 | CG | PRO- 455 | 4.37 | 0 | Hydrophobic |
| N25 | O | ARG- 498 | 2.9 | 176.03 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 501 | 3.7 | 0 | Hydrophobic |
| N2 | OD1 | ASP- 512 | 3.25 | 138.06 | H-Bond (Ligand Donor) |
| N25 | OD2 | ASP- 512 | 2.73 | 146.23 | H-Bond (Ligand Donor) |
| N25 | OD2 | ASP- 512 | 2.73 | 0 | Ionic (Ligand Cationic) |
| N25 | OD1 | ASP- 512 | 3.59 | 0 | Ionic (Ligand Cationic) |
