sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-06-14
| 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 | 36 % |
| B | 64 % |
| B-Factor: | 19.298 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.865 | 705.375 |
| % Hydrophobic | % Polar |
|---|---|
| 46.41 | 53.59 |
| According to VolSite | |
| HET Code: | RZW |
|---|---|
| Formula: | C14H17NO4 |
| Molecular weight: | 263.289 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.2 % |
| Polar Surface area: | 48 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 22.9826 | -17.1373 | -14.6414 |
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 |
| C15 | CE3 | TRP- 105 | 3.62 | 0 | Hydrophobic |
| C17 | CZ2 | TRP- 105 | 3.28 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 106 | 3.94 | 0 | Hydrophobic |
| C15 | CE1 | PHE- 106 | 3.59 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 126 | 3.44 | 0 | Hydrophobic |
| C19 | CE2 | PHE- 126 | 3.57 | 0 | Hydrophobic |
| C13 | CZ | TYR- 155 | 4.44 | 0 | Hydrophobic |
| O12 | ND2 | ASN- 161 | 2.82 | 158.9 | H-Bond (Protein Donor) |
| C13 | CE1 | PHE- 178 | 3.92 | 0 | Hydrophobic |
| C15 | CG | PHE- 178 | 3.83 | 0 | Hydrophobic |
| C17 | CE2 | PHE- 178 | 4.49 | 0 | Hydrophobic |
| C6 | C1' | FAD- 231 | 4.18 | 0 | Hydrophobic |
| C11 | C1' | FAD- 231 | 4.45 | 0 | Hydrophobic |
| C17 | C6 | FAD- 231 | 3.52 | 0 | Hydrophobic |
