sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2003-05-22
| Name: | Ribonucleoside-diphosphate reductase 2 subunit alpha |
|---|---|
| ID: | RIR3_SALTY |
| AC: | Q08698 |
| Organism: | Salmonella typhimurium |
| Reign: | Bacteria |
| TaxID: | 99287 |
| EC Number: | 1.17.4.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.818 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.377 | 340.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.42 | 41.58 |
| According to VolSite | |
| HET Code: | TTP |
|---|---|
| Formula: | C10H13N2O14P3 |
| Molecular weight: | 478.137 g/mol |
| DrugBank ID: | DB02452 |
| Buried Surface Area: | 46.79 % |
| Polar Surface area: | 279.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -3.3779 | 17.3023 | 149.678 |
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 |
| O3' | OD2 | ASP- 185 | 2.7 | 162.62 | H-Bond (Ligand Donor) |
| O1A | N | MET- 187 | 3.32 | 156.84 | H-Bond (Protein Donor) |
| C2' | SD | MET- 187 | 4.47 | 0 | Hydrophobic |
| C5M | CE | MET- 187 | 4.18 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 190 | 3.77 | 0 | Hydrophobic |
| O2G | CZ | ARG- 215 | 3.96 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 215 | 3.54 | 0 | Ionic (Protein Cationic) |
| O2G | NH1 | ARG- 215 | 3.06 | 170.18 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 215 | 2.87 | 152.13 | H-Bond (Protein Donor) |
| O3G | NH1 | ARG- 215 | 3.39 | 129.71 | H-Bond (Protein Donor) |
| C4' | CD | ARG- 215 | 3.76 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 221 | 4.08 | 0 | Hydrophobic |
| O2G | N | LYS- 222 | 2.82 | 171.34 | H-Bond (Protein Donor) |
| O2 | N | SER- 229 | 2.93 | 159.83 | H-Bond (Protein Donor) |
| O2A | MG | MG- 715 | 2.12 | 0 | Metal Acceptor |
| O1B | MG | MG- 715 | 1.86 | 0 | Metal Acceptor |
| O3G | MG | MG- 715 | 2.25 | 0 | Metal Acceptor |
