sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2005-08-22
| 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 | 60 % |
| B | 40 % |
| B-Factor: | 32.295 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.026 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 56.25 | 43.75 |
| According to VolSite | |
| HET Code: | CB1 |
|---|---|
| Formula: | C9H8N4O5 |
| Molecular weight: | 252.184 g/mol |
| DrugBank ID: | DB04253 |
| Buried Surface Area: | 61.36 % |
| Polar Surface area: | 137.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 30.5383 | 15.2336 | 32.4508 |
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 |
| C7 | CZ | PHE- 126 | 3.52 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 128 | 4.29 | 0 | Hydrophobic |
| O1 | ND2 | ASN- 161 | 3.4 | 126.17 | H-Bond (Protein Donor) |
| O2 | ND2 | ASN- 161 | 2.88 | 173.18 | H-Bond (Protein Donor) |
| C5 | C1' | FAD- 234 | 4.36 | 0 | Hydrophobic |
| C7 | C9A | FAD- 234 | 3.75 | 0 | Hydrophobic |
| C9 | C1' | FAD- 234 | 3.78 | 0 | Hydrophobic |
