sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2013-07-26
| 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: | 12.212 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.982 | 529.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.50 | 46.50 |
| According to VolSite | |
| HET Code: | 20O |
|---|---|
| Formula: | C21H18N2O3S |
| Molecular weight: | 378.444 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63 % |
| Polar Surface area: | 84.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 9.27278 | -6.49867 | 44.3753 |
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 |
| C24 | CB | ASP- 16 | 4.12 | 0 | Hydrophobic |
| C21 | CE2 | TYR- 18 | 4.26 | 0 | Hydrophobic |
| C20 | CD2 | TYR- 18 | 3.51 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 18 | 4 | 0 | Aromatic Face/Face |
| C11 | CB | HIS- 191 | 4.37 | 0 | Hydrophobic |
| C24 | CB | PHE- 193 | 4.39 | 0 | Hydrophobic |
| C21 | CZ | PHE- 193 | 3.35 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 193 | 3.78 | 0 | Aromatic Face/Face |
| C24 | CB | ASP- 219 | 3.86 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 242 | 3.75 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 242 | 3.85 | 0 | Hydrophobic |
| C19 | CB | ALA- 244 | 3.43 | 0 | Hydrophobic |
| C1 | CG | PRO- 273 | 4.02 | 0 | Hydrophobic |
| C6 | CB | PRO- 273 | 3.83 | 0 | Hydrophobic |
| C14 | CB | SER- 275 | 3.7 | 0 | Hydrophobic |
| O18 | OG | SER- 275 | 2.82 | 167.82 | H-Bond (Protein Donor) |
| C15 | CG2 | ILE- 309 | 4.09 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 309 | 3.76 | 0 | Hydrophobic |
| C20 | CD | ARG- 311 | 3.78 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 351 | 3.57 | 0 | Hydrophobic |
| N16 | O | HOH- 716 | 2.83 | 159.53 | H-Bond (Ligand Donor) |
