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
2015-12-04
| Name: | Single-stranded-DNA-specific exonuclease |
|---|---|
| ID: | D0EM60_DEIRD |
| AC: | D0EM60 |
| Organism: | Deinococcus radiodurans |
| Reign: | Bacteria |
| TaxID: | 1299 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 69.368 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MN MN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.873 | 1586.250 |
| % Hydrophobic | % Polar |
|---|---|
| 32.55 | 67.45 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.45 % |
| Polar Surface area: | 161.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -62.6267 | 29.8204 | 12.3054 |
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 |
| O3P | CZ | ARG- 109 | 3.82 | 0 | Ionic (Protein Cationic) |
| C2' | CD2 | TYR- 114 | 4.07 | 0 | Hydrophobic |
| C5M | CB | TYR- 114 | 4.16 | 0 | Hydrophobic |
| O2P | NH2 | ARG- 280 | 2.67 | 172.2 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 280 | 3.46 | 127.11 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 280 | 3.5 | 0 | Ionic (Protein Cationic) |
| O1P | OG | SER- 371 | 2.78 | 153.36 | H-Bond (Protein Donor) |
| O5' | OG | SER- 371 | 3.47 | 131.31 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 373 | 3.81 | 0 | Ionic (Protein Cationic) |
| O2P | NH2 | ARG- 373 | 2.88 | 165.19 | H-Bond (Protein Donor) |
| O5' | NH1 | ARG- 373 | 3.38 | 141.35 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 400 | 4.44 | 0 | Hydrophobic |
