sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2013-03-15
| Name: | Nicotinamide phosphoribosyltransferase |
|---|---|
| ID: | NAMPT_HUMAN |
| AC: | P43490 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 8 % |
| B | 92 % |
| B-Factor: | 10.396 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.866 | 1272.375 |
| % Hydrophobic | % Polar |
|---|---|
| 37.40 | 62.60 |
| According to VolSite | |
| HET Code: | 1LJ |
|---|---|
| Formula: | C19H18N4O3S |
| Molecular weight: | 382.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.88 % |
| Polar Surface area: | 122.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 9.43763 | -4.97596 | 44.3484 |
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 |
| C23 | CB | ASP- 16 | 4.48 | 0 | Hydrophobic |
| N27 | OD1 | ASP- 16 | 3.48 | 155.34 | H-Bond (Ligand Donor) |
| C22 | CB | TYR- 18 | 4.22 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 18 | 3.75 | 0 | Aromatic Face/Face |
| C23 | CB | ASP- 219 | 3.86 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 242 | 3.76 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 242 | 3.96 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 242 | 3.46 | 0 | Hydrophobic |
| C1 | CB | PRO- 273 | 3.8 | 0 | Hydrophobic |
| O18 | OG | SER- 275 | 3.13 | 138.43 | H-Bond (Protein Donor) |
| C12 | CB | SER- 275 | 3.59 | 0 | Hydrophobic |
| C6 | CG | PRO- 307 | 3.76 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 309 | 3.69 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 309 | 3.49 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 351 | 3.8 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 351 | 3.76 | 0 | Hydrophobic |
| N16 | O | HOH- 708 | 2.79 | 153.73 | H-Bond (Ligand Donor) |
