sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2012-01-24
| 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: | 44.738 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.165 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 56.63 | 43.37 |
| According to VolSite | |
| HET Code: | 0K0 |
|---|---|
| Formula: | C18H25N6O3S |
| Molecular weight: | 405.494 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.08 % |
| Polar Surface area: | 152.05 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: | 6 |
| X | Y | Z |
|---|---|---|
| 1.77221 | 1.45082 | 13.377 |
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 |
| C1 | CD1 | LEU- 377 | 4.04 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 377 | 3.83 | 0 | Hydrophobic |
| C4 | CB | LEU- 377 | 3.81 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 385 | 4.38 | 0 | Hydrophobic |
| N23 | O | GLU- 449 | 2.82 | 153.59 | H-Bond (Ligand Donor) |
| N10 | N | ALA- 451 | 3.01 | 176.47 | H-Bond (Protein Donor) |
| C27 | CG | PRO- 455 | 3.61 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 501 | 4.46 | 0 | Hydrophobic |
| C18 | CB | SER- 511 | 4.32 | 0 | Hydrophobic |
| C18 | CB | ASP- 512 | 4.35 | 0 | Hydrophobic |
| N22 | OD2 | ASP- 512 | 3 | 152.24 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 512 | 3 | 0 | Ionic (Ligand Cationic) |
