sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2006-05-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.520 | 9.520 | 9.520 | 0.000 | 9.520 | 1 |
| 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 | 90 % |
| B | 10 % |
| B-Factor: | 11.346 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.904 | 1339.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.05 | 59.95 |
| According to VolSite | |
| HET Code: | DGB |
|---|---|
| Formula: | C24H29N3O2 |
| Molecular weight: | 391.506 g/mol |
| DrugBank ID: | DB12731 |
| Buried Surface Area: | 66.22 % |
| 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 |
|---|---|---|
| 14.0673 | 5.59103 | -0.912931 |
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 |
| CAH | CB | ASP- 16 | 4.09 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 18 | 3.87 | 0 | Aromatic Face/Face |
| CAH | CB | PHE- 193 | 4.19 | 0 | Hydrophobic |
| CAJ | CB | ASP- 219 | 3.97 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 242 | 3.9 | 0 | Hydrophobic |
| CAO | CG2 | VAL- 242 | 3.59 | 0 | Hydrophobic |
| CAR | CB | PRO- 273 | 4.48 | 0 | Hydrophobic |
| OAA | OG | SER- 275 | 2.71 | 159.81 | H-Bond (Protein Donor) |
| CAL | CD1 | ILE- 309 | 4.16 | 0 | Hydrophobic |
| CAR | CD1 | ILE- 309 | 4.03 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 309 | 4.41 | 0 | Hydrophobic |
| CAK | CG | ARG- 349 | 3.92 | 0 | Hydrophobic |
| CAE | CD | ARG- 349 | 3.56 | 0 | Hydrophobic |
| CAG | CB | ARG- 349 | 3.42 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 351 | 4.25 | 0 | Hydrophobic |
| CAS | CB | ALA- 379 | 4.21 | 0 | Hydrophobic |
| CAG | CB | ALA- 379 | 3.55 | 0 | Hydrophobic |
