sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2007-01-03
| Name: | 3-methyladenine DNA glycosylase I |
|---|---|
| ID: | Q8Z2A5_SALTI |
| AC: | Q8Z2A5 |
| Organism: | Salmonella typhi |
| Reign: | Bacteria |
| TaxID: | 90370 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 29.545 |
|---|---|
| Number of residues: | 18 |
| Including | |
| Standard Amino Acids: | 14 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.343 | 303.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.22 | 57.78 |
| According to VolSite | |
| HET Code: | ADK |
|---|---|
| Formula: | C6H7N5 |
| Molecular weight: | 149.153 g/mol |
| DrugBank ID: | DB04104 |
| Buried Surface Area: | 66.8 % |
| Polar Surface area: | 69.62 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -5.80827 | 34.0833 | 46.5865 |
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 |
| N6 | OH | TYR- 16 | 3 | 168.93 | H-Bond (Ligand Donor) |
| N6 | OE2 | GLU- 38 | 2.75 | 155.88 | H-Bond (Ligand Donor) |
| N7 | OE1 | GLU- 38 | 2.57 | 159.67 | H-Bond (Ligand Donor) |
| N7 | OE2 | GLU- 38 | 3.48 | 132.66 | H-Bond (Ligand Donor) |
| C5 | CB | TRP- 46 | 3.75 | 0 | Hydrophobic |
| C5 | CB | SER- 164 | 4.44 | 0 | Hydrophobic |
