sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.840 Å
X-ray
2013-07-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.110 | 4.110 | 4.110 | 0.000 | 4.110 | 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 | 93 % |
| B | 7 % |
| B-Factor: | 11.687 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.909 | 1329.750 |
| % Hydrophobic | % Polar |
|---|---|
| 37.82 | 62.18 |
| According to VolSite | |
| HET Code: | 20N |
|---|---|
| Formula: | C12H14N2O2 |
| Molecular weight: | 218.252 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.82 % |
| Polar Surface area: | 58.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 14.5469 | 8.11781 | 0.131187 |
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 |
| C15 | CE1 | TYR- 18 | 3.9 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 18 | 3.76 | 0 | Hydrophobic |
| C15 | CZ | PHE- 193 | 3.54 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 242 | 3.95 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 242 | 4.31 | 0 | Hydrophobic |
| C14 | CB | ALA- 244 | 3.44 | 0 | Hydrophobic |
| O13 | OG | SER- 275 | 2.68 | 172.35 | H-Bond (Protein Donor) |
| C9 | CB | SER- 275 | 3.6 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 309 | 4 | 0 | Hydrophobic |
| C15 | CD | ARG- 311 | 4.12 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 351 | 3.47 | 0 | Hydrophobic |
| C1 | CB | ALA- 379 | 3.87 | 0 | Hydrophobic |
| N11 | O | HOH- 851 | 2.68 | 151.2 | H-Bond (Ligand Donor) |
