sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2007-12-08
| Name: | Tryptase alpha/beta-1 |
|---|---|
| ID: | TRYB1_HUMAN |
| AC: | Q15661 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.21.59 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 83 % |
| D | 17 % |
| B-Factor: | 20.891 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.148 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 25.93 | 74.07 |
| According to VolSite | |
| HET Code: | 11M |
|---|---|
| Formula: | C23H25N2O2S2 |
| Molecular weight: | 425.587 g/mol |
| DrugBank ID: | DB06848 |
| Buried Surface Area: | 52.9 % |
| Polar Surface area: | 110.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 40.5042 | -113.438 | -82.974 |
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 |
| C29 | CG | PRO- 48 | 3.82 | 0 | Hydrophobic |
| S59 | CE2 | TYR- 84 | 3.63 | 0 | Hydrophobic |
| C29 | CZ | TYR- 84 | 3.31 | 0 | Hydrophobic |
| S59 | CG2 | THR- 85 | 3.63 | 0 | Hydrophobic |
| S59 | CG | GLN- 87 | 3.7 | 0 | Hydrophobic |
| N64 | OD2 | ASP- 188 | 2.98 | 133.32 | H-Bond (Ligand Donor) |
| N64 | OD1 | ASP- 188 | 3.26 | 128.42 | H-Bond (Ligand Donor) |
| N64 | OD2 | ASP- 188 | 2.98 | 0 | Ionic (Ligand Cationic) |
| N64 | OD1 | ASP- 188 | 3.26 | 0 | Ionic (Ligand Cationic) |
| C5 | CB | SER- 189 | 4.18 | 0 | Hydrophobic |
| N64 | O | SER- 189 | 2.9 | 162.13 | H-Bond (Ligand Donor) |
| C8 | CB | GLN- 191 | 3.89 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 212 | 3.77 | 0 | Hydrophobic |
| C10 | CB | TRP- 214 | 4.37 | 0 | Hydrophobic |
| S59 | CZ3 | TRP- 214 | 3.99 | 0 | Hydrophobic |
| S44 | CG | GLU- 216 | 3.76 | 0 | Hydrophobic |
| C29 | CG | GLU- 216 | 4.36 | 0 | Hydrophobic |
| O61 | N | GLY- 217 | 2.86 | 157.03 | H-Bond (Protein Donor) |
| N64 | O | GLY- 217 | 3.17 | 168.42 | H-Bond (Ligand Donor) |
