sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2002-06-28
| Name: | N-glycosylase/DNA lyase |
|---|---|
| ID: | OGG1_HUMAN |
| AC: | O15527 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.2.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.796 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.354 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.00 | 55.00 |
| According to VolSite | |
| HET Code: | ANG |
|---|---|
| Formula: | C5H6N6O |
| Molecular weight: | 166.141 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.4 % |
| Polar Surface area: | 122.18 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 20.4909 | 23.2446 | 32.1405 |
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 |
| N7 | O | GLY- 42 | 2.63 | 172.44 | H-Bond (Ligand Donor) |
| N9 | NZ | LYS- 249 | 2.8 | 170.41 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 249 | 3.51 | 46.25 | Pi/Cation |
| N2 | OE1 | GLN- 315 | 2.75 | 142.14 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLN- 315 | 2.67 | 148.82 | H-Bond (Ligand Donor) |
