sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2009-02-12
| 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 | 89 % |
| B | 11 % |
| B-Factor: | 30.939 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.141 | 877.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.23 | 50.77 |
| According to VolSite | |
| HET Code: | IS1 |
|---|---|
| Formula: | C29H38N3O6 |
| Molecular weight: | 524.629 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.49 % |
| Polar Surface area: | 123.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 37.9054 | -6.64745 | -13.3402 |
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 |
| CAK | CB | ASP- 16 | 3.91 | 0 | Hydrophobic |
| CAK | CE2 | TYR- 18 | 3.25 | 0 | Hydrophobic |
| CAK | CB | PHE- 193 | 4.29 | 0 | Hydrophobic |
| C5' | CB | PHE- 193 | 4.49 | 0 | Hydrophobic |
| C3' | CD2 | PHE- 193 | 4.14 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 193 | 3.48 | 0 | Hydrophobic |
| CAL | CB | ASP- 219 | 4.44 | 0 | Hydrophobic |
| CAU | CG1 | VAL- 242 | 3.42 | 0 | Hydrophobic |
| CAS | CG2 | VAL- 242 | 3.82 | 0 | Hydrophobic |
| CAM | CD1 | ILE- 309 | 3.31 | 0 | Hydrophobic |
| OAA | NH1 | ARG- 311 | 3.49 | 149.77 | H-Bond (Protein Donor) |
| CAI | CB | ARG- 349 | 4.15 | 0 | Hydrophobic |
| CAJ | CD | ARG- 349 | 3.52 | 0 | Hydrophobic |
| CAI | CG2 | ILE- 351 | 3.73 | 0 | Hydrophobic |
| CAR | CD1 | ILE- 351 | 4.3 | 0 | Hydrophobic |
| CAM | CB | SER- 379 | 3.69 | 0 | Hydrophobic |
| CAH | CB | SER- 379 | 3.57 | 0 | Hydrophobic |
| O5' | NH1 | ARG- 392 | 3.49 | 167.4 | H-Bond (Protein Donor) |
