sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2013-08-10
| 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 | 89 % |
| B | 11 % |
| B-Factor: | 12.541 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.858 | 1380.375 |
| % Hydrophobic | % Polar |
|---|---|
| 36.67 | 63.33 |
| According to VolSite | |
| HET Code: | 20R |
|---|---|
| Formula: | C20H16N4O3S |
| Molecular weight: | 392.431 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.19 % |
| Polar Surface area: | 113.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.377 | 7.97989 | 1.82207 |
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 |
| DuAr | DuAr | TYR- 18 | 3.74 | 0 | Aromatic Face/Face |
| C15 | CB | HIS- 191 | 3.97 | 0 | Hydrophobic |
| C22 | CB | PHE- 193 | 4.18 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 193 | 3.59 | 0 | Aromatic Face/Face |
| N17 | OD1 | ASP- 219 | 3.44 | 128.56 | H-Bond (Ligand Donor) |
| N17 | OD2 | ASP- 219 | 2.84 | 149.92 | H-Bond (Ligand Donor) |
| C21 | CB | ASP- 219 | 4.32 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 242 | 3.92 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 242 | 3.73 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 242 | 3.45 | 0 | Hydrophobic |
| C12 | CB | ALA- 244 | 3.93 | 0 | Hydrophobic |
| C6 | CB | PRO- 273 | 4.44 | 0 | Hydrophobic |
| C12 | CB | SER- 275 | 3.67 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 309 | 3.91 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 351 | 4 | 0 | Hydrophobic |
