sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2006-03-05
| Name: | Nicotinamide phosphoribosyltransferase |
|---|---|
| ID: | NAMPT_RAT |
| AC: | Q80Z29 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 2.4.2.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 85 % |
| B | 15 % |
| B-Factor: | 23.898 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.869 | 1471.500 |
| % Hydrophobic | % Polar |
|---|---|
| 31.19 | 68.81 |
| According to VolSite | |
| HET Code: | NMN |
|---|---|
| Formula: | C11H14N2O8P |
| Molecular weight: | 333.211 g/mol |
| DrugBank ID: | DB03227 |
| Buried Surface Area: | 66.08 % |
| Polar Surface area: | 178.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 10.1858 | 96.8867 | 12.6136 |
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 |
| C5 | CB | ASP- 16 | 4 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 18 | 3.39 | 0 | Hydrophobic |
| C2R | CD2 | PHE- 193 | 3.63 | 0 | Hydrophobic |
| C5 | CB | PHE- 193 | 3.5 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 193 | 3.61 | 0 | Aromatic Face/Face |
| C5R | CD | ARG- 196 | 3.85 | 0 | Hydrophobic |
| C4 | CB | ASP- 219 | 4.08 | 0 | Hydrophobic |
| O2R | NH2 | ARG- 311 | 3 | 133.28 | H-Bond (Protein Donor) |
| O3R | OD2 | ASP- 313 | 2.84 | 144.41 | H-Bond (Ligand Donor) |
| O5R | NH2 | ARG- 392 | 2.89 | 164.21 | H-Bond (Protein Donor) |
