sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.710 Å
X-ray
2013-12-15
| 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 | 91 % |
| B | 9 % |
| B-Factor: | 11.466 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 6 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.763 | 1302.750 |
| % Hydrophobic | % Polar |
|---|---|
| 35.49 | 64.51 |
| According to VolSite | |
| HET Code: | DGB |
|---|---|
| Formula: | C24H29N3O2 |
| Molecular weight: | 391.506 g/mol |
| DrugBank ID: | DB12731 |
| Buried Surface Area: | 56.77 % |
| 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 |
|---|---|---|
| 15.249 | 6.89931 | -1.53272 |
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 | 3.99 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 18 | 3.78 | 0 | Aromatic Face/Face |
| DuAr | DuAr | PHE- 193 | 3.94 | 0 | Aromatic Face/Face |
| CAH | CB | PHE- 193 | 4.09 | 0 | Hydrophobic |
| CAH | CB | ASP- 219 | 3.98 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 242 | 3.51 | 0 | Hydrophobic |
| CAS | CB | PRO- 273 | 4.25 | 0 | Hydrophobic |
| CAG | CG | PRO- 273 | 3.32 | 0 | Hydrophobic |
| OAA | OG | SER- 275 | 2.73 | 163.94 | H-Bond (Protein Donor) |
| CAF | CG | PRO- 307 | 4.09 | 0 | Hydrophobic |
| CAS | CD1 | ILE- 309 | 3.45 | 0 | Hydrophobic |
| CBB | CG1 | ILE- 309 | 4 | 0 | Hydrophobic |
| CAQ | CD1 | ILE- 309 | 3.99 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 351 | 3.55 | 0 | Hydrophobic |
| CAR | CB | ALA- 379 | 4.22 | 0 | Hydrophobic |
| NAW | O | HOH- 779 | 2.75 | 149.3 | H-Bond (Ligand Donor) |
