sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-01-07
| Name: | Toxin zeta |
|---|---|
| ID: | ZTOX_STRPY |
| AC: | Q54944 |
| Organism: | Streptococcus pyogenes |
| Reign: | Bacteria |
| TaxID: | 1314 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 83.898 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.889 | 1009.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.47 | 58.53 |
| According to VolSite | |
| HET Code: | UD1 |
|---|---|
| Formula: | C17H25N3O17P2 |
| Molecular weight: | 605.338 g/mol |
| DrugBank ID: | DB03397 |
| Buried Surface Area: | 45.14 % |
| Polar Surface area: | 325.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 7 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -18.1822 | 36.505 | 56.9524 |
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 |
| C8' | CB | ASN- 66 | 4.25 | 0 | Hydrophobic |
| O4B | ND2 | ASN- 66 | 2.79 | 151.06 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 67 | 3.04 | 174.67 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 67 | 3.39 | 128.89 | H-Bond (Ligand Donor) |
| C1B | CG2 | THR- 99 | 4.1 | 0 | Hydrophobic |
| O2' | OE2 | GLU- 100 | 3.13 | 156.32 | H-Bond (Ligand Donor) |
| C8' | CG | GLU- 116 | 3.27 | 0 | Hydrophobic |
| O1A | N | THR- 118 | 3.03 | 148.98 | H-Bond (Protein Donor) |
| O2B | OG1 | THR- 118 | 2.79 | 148.7 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 120 | 2.92 | 148.25 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 120 | 3.47 | 142.2 | H-Bond (Protein Donor) |
| O2B | NE | ARG- 120 | 3.18 | 160.97 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 120 | 3.96 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 120 | 3.78 | 0 | Ionic (Protein Cationic) |
| C3B | CG2 | VAL- 124 | 4.29 | 0 | Hydrophobic |
| N3 | OG1 | THR- 128 | 3.14 | 121.81 | H-Bond (Ligand Donor) |
