sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.530 Å
X-ray
2014-03-14
| Name: | Genome polyprotein |
|---|---|
| ID: | A9LIE0_9FLAV |
| AC: | A9LIE0 |
| Organism: | Dengue virus 3 |
| Reign: | Viruses |
| TaxID: | 11069 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.011 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.680 | 867.375 |
| % Hydrophobic | % Polar |
|---|---|
| 34.63 | 65.37 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 65.26 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 31.9324 | 42.0088 | -6.10363 |
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 |
| OXT | OG | SER- 56 | 2.76 | 160.44 | H-Bond (Protein Donor) |
| OXT | N | GLY- 86 | 3.1 | 147.09 | H-Bond (Protein Donor) |
| N3 | N | LYS- 105 | 3.11 | 130.83 | H-Bond (Protein Donor) |
| O2' | ND1 | HIS- 110 | 2.64 | 172.48 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 111 | 2.81 | 160.34 | H-Bond (Ligand Donor) |
| N6 | OD1 | ASP- 131 | 2.89 | 158.49 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 132 | 3.03 | 166.78 | H-Bond (Protein Donor) |
| N | OD2 | ASP- 146 | 2.86 | 169.47 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 146 | 2.86 | 0 | Ionic (Ligand Cationic) |
| CG | CB | ASP- 146 | 4.02 | 0 | Hydrophobic |
