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 | 88 % |
| B | 12 % |
| B-Factor: | 15.653 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.029 | 759.375 |
| % Hydrophobic | % Polar |
|---|---|
| 47.56 | 52.44 |
| According to VolSite | |
| HET Code: | DGB |
|---|---|
| Formula: | C24H29N3O2 |
| Molecular weight: | 391.506 g/mol |
| DrugBank ID: | DB12731 |
| Buried Surface Area: | 62.69 % |
| Polar Surface area: | 62.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 0.473103 | 101.038 | 13.615 |
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 |
| CAN | CB | HIS- 191 | 3.99 | 0 | Hydrophobic |
| CAN | CE1 | PHE- 193 | 4.48 | 0 | Hydrophobic |
| CAH | CB | PHE- 193 | 4.18 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 193 | 3.35 | 0 | Aromatic Face/Face |
| CAR | CG2 | VAL- 242 | 3.8 | 0 | Hydrophobic |
| CBB | CG1 | VAL- 242 | 4.06 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 242 | 3.36 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 309 | 4.38 | 0 | Hydrophobic |
| CAK | CD1 | ILE- 309 | 3.96 | 0 | Hydrophobic |
| CAR | CD1 | ILE- 309 | 3.42 | 0 | Hydrophobic |
| CAJ | CD | ARG- 311 | 4.31 | 0 | Hydrophobic |
| CAE | CD | ARG- 349 | 3.33 | 0 | Hydrophobic |
| CBA | CG | ARG- 349 | 3.96 | 0 | Hydrophobic |
| CAF | CB | ARG- 349 | 3.6 | 0 | Hydrophobic |
| CAG | CD | ARG- 349 | 3.61 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 351 | 4.43 | 0 | Hydrophobic |
| CAK | CB | SER- 379 | 3.66 | 0 | Hydrophobic |
| CAE | CB | SER- 379 | 3.93 | 0 | Hydrophobic |
| CAS | CB | SER- 379 | 4.31 | 0 | Hydrophobic |
