sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2013-12-04
| Name: | 7-methylguanosine phosphate-specific 5'-nucleotidase |
|---|---|
| ID: | 5NT3B_DROME |
| AC: | Q9W197 |
| Organism: | Drosophila melanogaster |
| Reign: | Eukaryota |
| TaxID: | 7227 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| B | 96 % |
| B-Factor: | 18.352 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.373 | 2055.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.04 | 57.96 |
| According to VolSite | |
| HET Code: | MG7 |
|---|---|
| Formula: | C11H16N5O5 |
| Molecular weight: | 298.275 g/mol |
| DrugBank ID: | DB03493 |
| Buried Surface Area: | 64.4 % |
| Polar Surface area: | 146.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -37.9844 | 6.88376 | -23.1798 |
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 | ASP- 57 | 3.93 | 0 | Hydrophobic |
| C4' | CB | SER- 73 | 4.24 | 0 | Hydrophobic |
| CN7 | CZ | PHE- 75 | 4.03 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 75 | 3.9 | 0 | Aromatic Face/Face |
| O2' | OE1 | GLU- 103 | 3.44 | 136.57 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 103 | 2.66 | 156.01 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 103 | 2.63 | 164.64 | H-Bond (Ligand Donor) |
| O3' | OE2 | GLU- 103 | 3.47 | 129.22 | H-Bond (Ligand Donor) |
| CN7 | CE2 | TRP- 120 | 3.57 | 0 | Hydrophobic |
| C2' | CH2 | TRP- 120 | 3.68 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 120 | 3.78 | 0 | Aromatic Face/Face |
| CN7 | CD2 | TRP- 121 | 3.96 | 0 | Hydrophobic |
| C3' | CH2 | TRP- 121 | 3.85 | 0 | Hydrophobic |
| CN7 | CB | SER- 124 | 3.91 | 0 | Hydrophobic |
| O6 | O | HOH- 693 | 2.84 | 179.96 | H-Bond (Protein Donor) |
