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
2012-02-20
| Name: | APH(2'')-Id |
|---|---|
| ID: | O68183_ENTCA |
| AC: | O68183 |
| Organism: | Enterococcus casseliflavus |
| Reign: | Bacteria |
| TaxID: | 37734 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.291 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.068 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 31.33 | 68.67 |
| According to VolSite | |
| HET Code: | GMP |
|---|---|
| Formula: | C10H13N5O5 |
| Molecular weight: | 283.241 g/mol |
| DrugBank ID: | DB02857 |
| Buried Surface Area: | 65.36 % |
| Polar Surface area: | 155.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 2.2652 | 8.05855 | 29.1918 |
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 |
| C5' | CB | ALA- 36 | 4.04 | 0 | Hydrophobic |
| O6 | N | ILE- 98 | 2.88 | 168.61 | H-Bond (Protein Donor) |
| N1 | O | ILE- 98 | 2.71 | 161.9 | H-Bond (Ligand Donor) |
| N2 | O | ILE- 98 | 3.37 | 129.69 | H-Bond (Ligand Donor) |
| C2' | CD1 | ILE- 216 | 3.75 | 0 | Hydrophobic |
| O5' | OD1 | ASP- 217 | 2.81 | 150.33 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 217 | 2.64 | 158.51 | H-Bond (Ligand Donor) |
