sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.920 Å
X-ray
2007-07-31
| Name: | Nicotinamide riboside kinase 1 |
|---|---|
| ID: | NRK1_HUMAN |
| AC: | Q9NWW6 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.454 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ANP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.305 | 394.875 |
| % Hydrophobic | % Polar |
|---|---|
| 52.99 | 47.01 |
| According to VolSite | |
| HET Code: | NNR |
|---|---|
| Formula: | C11H15N2O5 |
| Molecular weight: | 255.247 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.04 % |
| Polar Surface area: | 116.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -18.0603 | 0.436111 | -10.7699 |
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 |
| C4R | CB | THR- 12 | 4.35 | 0 | Hydrophobic |
| C5R | CZ | PHE- 39 | 4.11 | 0 | Hydrophobic |
| C2R | CB | TYR- 55 | 4.16 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 55 | 3.44 | 0 | Hydrophobic |
| O3R | OD2 | ASP- 56 | 2.52 | 162.22 | H-Bond (Ligand Donor) |
| O3R | OD1 | ASP- 56 | 3.35 | 122.15 | H-Bond (Ligand Donor) |
| C3R | CE1 | PHE- 100 | 3.81 | 0 | Hydrophobic |
| C5R | CG | PHE- 100 | 3.85 | 0 | Hydrophobic |
| O2R | NH2 | ARG- 129 | 2.94 | 172.28 | H-Bond (Protein Donor) |
| O3R | NH1 | ARG- 129 | 2.83 | 152.44 | H-Bond (Protein Donor) |
| C4R | CE1 | TYR- 134 | 4.04 | 0 | Hydrophobic |
| C5 | CB | TYR- 134 | 3.91 | 0 | Hydrophobic |
| O5R | O1G | ANP- 1102 | 3.28 | 162.39 | H-Bond (Ligand Donor) |
