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
2010-09-20
| Name: | Ribosyldihydronicotinamide dehydrogenase [quinone] |
|---|---|
| ID: | NQO2_HUMAN |
| AC: | P16083 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 25.408 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.641 | 600.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.31 | 51.69 |
| According to VolSite | |
| HET Code: | XRA |
|---|---|
| Formula: | C19H21N5O4 |
| Molecular weight: | 383.401 g/mol |
| DrugBank ID: | DB00457 |
| Buried Surface Area: | 49.56 % |
| Polar Surface area: | 106.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 26.3347 | -16.3728 | -16.2856 |
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 |
| C14 | CZ3 | TRP- 105 | 3.62 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 106 | 3.69 | 0 | Hydrophobic |
| C12 | SD | MET- 154 | 3.83 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 161 | 2.61 | 156.76 | H-Bond (Protein Donor) |
| C14 | CD1 | PHE- 178 | 3.66 | 0 | Hydrophobic |
| C3 | C1' | FAD- 232 | 4.36 | 0 | Hydrophobic |
| C21 | C1' | FAD- 232 | 3.92 | 0 | Hydrophobic |
