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
1995-11-21
| Name: | Pertussis toxin subunit 4 | Pertussis toxin subunit 5 |
|---|---|---|
| ID: | TOX4_BORPE | TOX5_BORPE |
| AC: | P0A3R5 | P04981 |
| Organism: | Bordetella pertussis | |
| Reign: | Bacteria | |
| TaxID: | 257313 | |
| EC Number: | / | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 5 % |
| B | 8 % |
| C | 11 % |
| D | 8 % |
| E | 37 % |
| F | 32 % |
| B-Factor: | 8.775 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.336 | 671.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.26 | 47.74 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 71.31 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -9.8469 | 13.9461 | -14.83 |
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 |
| C4' | CE | MET- 18 | 4.09 | 0 | Hydrophobic |
| C1' | CE | MET- 18 | 3.9 | 0 | Hydrophobic |
| C4' | CG2 | THR- 55 | 3.66 | 0 | Hydrophobic |
| O2' | OG | SER- 61 | 3.07 | 161.97 | H-Bond (Protein Donor) |
| O2B | NH1 | ARG- 69 | 3.25 | 125.97 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 69 | 2.85 | 157.85 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 69 | 3.18 | 138.13 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 69 | 3.45 | 0 | Ionic (Protein Cationic) |
| O2' | O | HOH- 114 | 3.06 | 145.62 | H-Bond (Ligand Donor) |
| O3G | NH2 | ARG- 150 | 3.12 | 158.03 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 150 | 3.24 | 126.01 | H-Bond (Protein Donor) |
| O3B | NH2 | ARG- 150 | 3.35 | 168.94 | H-Bond (Protein Donor) |
| O2G | CZ | ARG- 151 | 3.89 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 151 | 3.61 | 0 | Ionic (Protein Cationic) |
| O2G | NH2 | ARG- 151 | 2.8 | 126.4 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 151 | 3.01 | 138.45 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 151 | 3.01 | 0 | Ionic (Protein Cationic) |
| O2A | N | PHE- 235 | 3.2 | 141.23 | H-Bond (Protein Donor) |
