sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 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 | 7 % |
| B | 93 % |
| B-Factor: | 6.512 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 8 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.575 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.35 | 51.65 |
| According to VolSite | |
| HET Code: | DGB |
|---|---|
| Formula: | C24H29N3O2 |
| Molecular weight: | 391.506 g/mol |
| DrugBank ID: | DB12731 |
| Buried Surface Area: | 65.37 % |
| 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 |
|---|---|---|
| 8.1111 | -3.75745 | 45.7772 |
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 | 3.96 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 18 | 3.82 | 0 | Aromatic Face/Face |
| CAL | CB | TYR- 188 | 3.87 | 0 | Hydrophobic |
| CAL | CD | LYS- 189 | 4.25 | 0 | Hydrophobic |
| OAB | NZ | LYS- 189 | 2.85 | 152.55 | H-Bond (Protein Donor) |
| CAH | CB | PHE- 193 | 4.15 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 193 | 3.94 | 0 | Aromatic Face/Face |
| CAH | CB | ASP- 219 | 3.73 | 0 | Hydrophobic |
| CAQ | CG2 | VAL- 242 | 4.1 | 0 | Hydrophobic |
| CAO | CG1 | VAL- 242 | 4.09 | 0 | Hydrophobic |
| CAN | CB | VAL- 242 | 4.01 | 0 | Hydrophobic |
| OAA | OG | SER- 275 | 2.71 | 163.05 | H-Bond (Protein Donor) |
| CAO | CB | SER- 275 | 4.36 | 0 | Hydrophobic |
| CAS | CG2 | ILE- 309 | 4.03 | 0 | Hydrophobic |
| CBB | CG1 | ILE- 309 | 3.84 | 0 | Hydrophobic |
| CAO | CD1 | ILE- 309 | 4.24 | 0 | Hydrophobic |
| CAS | CB | ILE- 351 | 4.46 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 351 | 3.72 | 0 | Hydrophobic |
| CAS | CB | ALA- 379 | 3.48 | 0 | Hydrophobic |
| NAW | O | HOH- 735 | 2.73 | 138.79 | H-Bond (Ligand Donor) |
