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
2004-01-08
| Name: | Nucleoside 2-deoxyribosyltransferase |
|---|---|
| ID: | Q8RLY5_LACHE |
| AC: | Q8RLY5 |
| Organism: | Lactobacillus helveticus |
| Reign: | Bacteria |
| TaxID: | 1587 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 33.263 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.640 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.70 | 43.30 |
| According to VolSite | |
| HET Code: | 3D1 |
|---|---|
| Formula: | C10H13N5O3 |
| Molecular weight: | 251.242 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.4 % |
| Polar Surface area: | 119.31 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -23.2648 | -3.78467 | 6.522 |
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' | N | SER- 14 | 3.03 | 148.01 | H-Bond (Protein Donor) |
| C2' | CG | PRO- 44 | 3.54 | 0 | Hydrophobic |
| C5' | CZ | PHE- 45 | 3.98 | 0 | Hydrophobic |
| C3' | CE1 | PHE- 45 | 3.72 | 0 | Hydrophobic |
| O5' | OD1 | ASP- 95 | 2.77 | 126.86 | H-Bond (Ligand Donor) |
| O5' | OD2 | ASP- 95 | 2.63 | 160.34 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 101 | 2.55 | 158.24 | H-Bond (Ligand Donor) |
