sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.320 Å
X-ray
2003-12-01
| Name: | ADP compounds hydrolase NudE |
|---|---|
| ID: | NUDE_ECOLI |
| AC: | P45799 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 3.6.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 35 % |
| B | 65 % |
| B-Factor: | 32.972 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.196 | 2554.875 |
| % Hydrophobic | % Polar |
|---|---|
| 43.20 | 56.80 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.3 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 42.2534 | 17.315 | 147.566 |
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 |
| C2' | CZ | TYR- 39 | 3.88 | 0 | Hydrophobic |
| N1 | N | GLU- 40 | 2.98 | 164.15 | H-Bond (Protein Donor) |
| N6 | O | GLU- 40 | 2.8 | 155.84 | H-Bond (Ligand Donor) |
| N6 | O | SER- 118 | 3.12 | 138.54 | H-Bond (Ligand Donor) |
