sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2008-09-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.050 | 8.050 | 8.050 | 0.000 | 8.050 | 1 |
| 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: | 19.983 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.902 | 499.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.70 | 47.30 |
| According to VolSite | |
| HET Code: | 685 |
|---|---|
| Formula: | C20H23N5O2S |
| Molecular weight: | 397.494 g/mol |
| DrugBank ID: | DB07194 |
| Buried Surface Area: | 60 % |
| Polar Surface area: | 128.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 13.6799 | 42.1645 | 10.8246 |
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 |
| C25 | CB | LEU- 377 | 3.6 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 377 | 4.23 | 0 | Hydrophobic |
| C1 | CZ | PHE- 382 | 3.49 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 382 | 4.29 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 385 | 4.15 | 0 | Hydrophobic |
| S10 | CG1 | VAL- 385 | 3.89 | 0 | Hydrophobic |
| C16 | CB | ALA- 400 | 4.11 | 0 | Hydrophobic |
| O8 | NZ | LYS- 402 | 2.5 | 149.48 | H-Bond (Protein Donor) |
| C14 | CD | LYS- 402 | 4.27 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 433 | 4.1 | 0 | Hydrophobic |
| S10 | CE | MET- 448 | 4.44 | 0 | Hydrophobic |
| C14 | SD | MET- 448 | 4.15 | 0 | Hydrophobic |
| C16 | CE | MET- 448 | 3.58 | 0 | Hydrophobic |
| C28 | CE | MET- 450 | 3.48 | 0 | Hydrophobic |
| N18 | N | ALA- 451 | 3.1 | 170.78 | H-Bond (Protein Donor) |
| N20 | O | ALA- 451 | 3.18 | 141.73 | H-Bond (Ligand Donor) |
| C16 | CD1 | LEU- 501 | 3.33 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 501 | 3.75 | 0 | Hydrophobic |
| C14 | CB | ASP- 512 | 4.3 | 0 | Hydrophobic |
