sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.190 Å
X-ray
2012-06-14
| 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: | 48.993 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.600 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.37 | 48.63 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.87 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -26.8098 | -9.68152 | -5.85974 |
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' | CB | LEU- 377 | 4.35 | 0 | Hydrophobic |
| O3G | N | ASN- 381 | 2.68 | 160.66 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 385 | 4.37 | 0 | Hydrophobic |
| C1' | CB | VAL- 385 | 4.22 | 0 | Hydrophobic |
| O1A | NZ | LYS- 402 | 3.27 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 402 | 2.79 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 402 | 2.79 | 156.36 | H-Bond (Protein Donor) |
| N6 | O | GLU- 449 | 2.89 | 166 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 451 | 3.04 | 156.26 | H-Bond (Protein Donor) |
| C3' | CG | PRO- 455 | 4.41 | 0 | Hydrophobic |
| O1G | CZ | ARG- 498 | 3.97 | 0 | Ionic (Protein Cationic) |
| O1G | NE | ARG- 498 | 3.1 | 154.7 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 501 | 4.33 | 0 | Hydrophobic |
| O1G | OH | TYR- 525 | 3.33 | 163.13 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 533 | 3.65 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 533 | 2.65 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 533 | 2.65 | 157.61 | H-Bond (Protein Donor) |
| O1B | MG | MG- 701 | 2.12 | 0 | Metal Acceptor |
| O2A | MG | MG- 701 | 2.21 | 0 | Metal Acceptor |
