sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-03-27
| Name: | 5'-deoxynucleotidase YfbR |
|---|---|
| ID: | 5DNU_ECOLI |
| AC: | P76491 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.690 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.141 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.84 | 60.16 |
| According to VolSite | |
| HET Code: | TMP |
|---|---|
| Formula: | C10H13N2O8P |
| Molecular weight: | 320.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.06 % |
| 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 |
|---|---|---|
| -20.4696 | -5.61452 | 8.624 |
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- 18 | 3.81 | 0 | Ionic (Protein Cationic) |
| O3P | NH1 | ARG- 18 | 2.81 | 159.27 | H-Bond (Protein Donor) |
| O5' | NH1 | ARG- 18 | 3.27 | 125.12 | H-Bond (Protein Donor) |
| C3' | CB | ARG- 18 | 4.07 | 0 | Hydrophobic |
| O3' | N | TRP- 19 | 2.96 | 153.36 | H-Bond (Protein Donor) |
| C2' | CE2 | TRP- 19 | 3.75 | 0 | Hydrophobic |
| C1' | CE3 | TRP- 19 | 4.36 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 77 | 2.87 | 145.68 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 77 | 2.52 | 141.72 | H-Bond (Ligand Donor) |
| O4' | N | THR- 80 | 3.4 | 170.13 | H-Bond (Protein Donor) |
| C1' | CG2 | THR- 80 | 4.39 | 0 | Hydrophobic |
| C5' | CG2 | THR- 80 | 3.99 | 0 | Hydrophobic |
| C5M | CB | ALA- 141 | 3.69 | 0 | Hydrophobic |
| C5M | CD2 | LEU- 163 | 3.74 | 0 | Hydrophobic |
