sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-11-19
| 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: | 17.505 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.072 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.97 | 46.03 |
| According to VolSite | |
| HET Code: | 1B6 |
|---|---|
| Formula: | C18H22N6O |
| Molecular weight: | 338.407 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.71 % |
| Polar Surface area: | 88.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 1.61316 | 0.93608 | 14.0746 |
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 |
| C16 | CD2 | PHE- 382 | 4.04 | 0 | Hydrophobic |
| C21 | CD2 | PHE- 382 | 4.31 | 0 | Hydrophobic |
| C24 | CZ | PHE- 382 | 4.13 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 385 | 4.08 | 0 | Hydrophobic |
| C24 | CB | VAL- 385 | 4.49 | 0 | Hydrophobic |
| C16 | CD | LYS- 402 | 4.01 | 0 | Hydrophobic |
| N9 | O | GLU- 449 | 2.89 | 173.55 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 451 | 3.15 | 168.22 | H-Bond (Protein Donor) |
| C25 | CG | PRO- 455 | 4.13 | 0 | Hydrophobic |
| C22 | CG | PRO- 455 | 4.18 | 0 | Hydrophobic |
| O13 | OG | SER- 511 | 2.79 | 170.54 | H-Bond (Protein Donor) |
| C15 | CB | SER- 511 | 4.34 | 0 | Hydrophobic |
| C15 | CB | ASP- 512 | 3.92 | 0 | Hydrophobic |
