sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.870 Å
X-ray
2015-05-18
| 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 | 31 % |
| B | 69 % |
| B-Factor: | 18.137 |
|---|---|
| Number of residues: | 56 |
| Including | |
| Standard Amino Acids: | 54 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.104 | 1090.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.99 | 52.01 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 66.86 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -3.13919 | -2.06449 | -6.82562 |
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 |
| O1P | NE2 | HIS- 11 | 2.78 | 157.66 | H-Bond (Protein Donor) |
| O2A | N | PHE- 17 | 3.05 | 156.71 | H-Bond (Protein Donor) |
| C5B | CB | PHE- 17 | 4.12 | 0 | Hydrophobic |
| C1B | CD1 | PHE- 17 | 4.33 | 0 | Hydrophobic |
| O2P | ND2 | ASN- 18 | 2.8 | 167.85 | H-Bond (Protein Donor) |
| O2P | N | ASN- 18 | 2.95 | 148.49 | H-Bond (Protein Donor) |
| N6A | OG | SER- 20 | 3.01 | 158.14 | H-Bond (Ligand Donor) |
| C8M | CD2 | TYR- 67 | 3.79 | 0 | Hydrophobic |
| C2' | CB | PRO- 102 | 4.46 | 0 | Hydrophobic |
| C4' | CB | PRO- 102 | 3.65 | 0 | Hydrophobic |
| O2' | O | LEU- 103 | 2.73 | 159.93 | H-Bond (Ligand Donor) |
| C7M | CD2 | TYR- 104 | 3.94 | 0 | Hydrophobic |
| C8M | CE1 | TYR- 104 | 3.67 | 0 | Hydrophobic |
| C6 | CB | TYR- 104 | 3.98 | 0 | Hydrophobic |
| N5 | N | TRP- 105 | 2.87 | 173.33 | H-Bond (Protein Donor) |
| O4 | N | PHE- 106 | 3.06 | 140.44 | H-Bond (Protein Donor) |
| C7M | CB | ASP- 117 | 4.37 | 0 | Hydrophobic |
| O4' | OG1 | THR- 147 | 2.62 | 169.46 | H-Bond (Protein Donor) |
| N1 | N | GLY- 149 | 3.02 | 146.15 | H-Bond (Protein Donor) |
| O2 | N | GLY- 149 | 3.16 | 122.09 | H-Bond (Protein Donor) |
| O2 | N | GLY- 150 | 2.76 | 161.5 | H-Bond (Protein Donor) |
| O2 | OH | TYR- 155 | 2.6 | 170.54 | H-Bond (Protein Donor) |
| N3 | OH | TYR- 155 | 2.99 | 127.58 | H-Bond (Ligand Donor) |
| C5B | CB | PRO- 192 | 4.13 | 0 | Hydrophobic |
| C5' | CG | PRO- 192 | 4.43 | 0 | Hydrophobic |
| C5B | CG | GLU- 193 | 4.05 | 0 | Hydrophobic |
| C5' | CG | GLU- 193 | 4.32 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 193 | 3.17 | 129.18 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 193 | 2.64 | 164.98 | H-Bond (Ligand Donor) |
| C4B | CD | ARG- 200 | 3.79 | 0 | Hydrophobic |
| C1B | CD | ARG- 200 | 4.04 | 0 | Hydrophobic |
| N3A | NE | ARG- 200 | 3.08 | 169.44 | H-Bond (Protein Donor) |
| N1A | NZ | LYS- 201 | 3.37 | 160.63 | H-Bond (Protein Donor) |
