sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2007-05-22
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1N5 |
| AC: | P12497 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11698 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.000 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 239.625 |
| % Hydrophobic | % Polar |
|---|---|
| 74.65 | 25.35 |
| According to VolSite | |
| HET Code: | JPR |
|---|---|
| Formula: | C18H25ClN3O2S |
| Molecular weight: | 382.928 g/mol |
| DrugBank ID: | DB08027 |
| Buried Surface Area: | 39.56 % |
| Polar Surface area: | 84.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -31.1581 | 10.6293 | -4.13708 |
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 |
| C7 | CG1 | VAL- 27 | 3.4 | 0 | Hydrophobic |
| N3 | OE1 | GLU- 28 | 3.96 | 0 | Ionic (Ligand Cationic) |
| N3 | OE2 | GLU- 28 | 2.75 | 0 | Ionic (Ligand Cationic) |
| N3 | OE2 | GLU- 28 | 2.75 | 174.87 | H-Bond (Ligand Donor) |
| C5 | CB | ALA- 31 | 3.56 | 0 | Hydrophobic |
| N1 | O | VAL- 59 | 2.81 | 159.33 | H-Bond (Ligand Donor) |
| C7 | CB | VAL- 59 | 4.49 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 59 | 3.88 | 0 | Hydrophobic |
| N2 | N | HIS- 62 | 3.49 | 133.51 | H-Bond (Protein Donor) |
| C7 | CB | HIS- 62 | 4.01 | 0 | Hydrophobic |
| C3 | CB | ALA- 65 | 3.79 | 0 | Hydrophobic |
| CL1 | CE | MET- 66 | 4.35 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 69 | 3.81 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 138 | 4.02 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 138 | 3.49 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 141 | 3.71 | 0 | Hydrophobic |
