sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1996-12-05
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 56 % |
| B | 44 % |
| B-Factor: | 13.239 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.780 | 840.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.98 | 55.02 |
| According to VolSite | |
| HET Code: | INU |
|---|---|
| Formula: | C27H28NO5S |
| Molecular weight: | 478.580 g/mol |
| DrugBank ID: | DB02033 |
| Buried Surface Area: | 56.47 % |
| Polar Surface area: | 103.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 11.5409 | 25.4787 | 5.65771 |
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 |
| DuAr | CZ | ARG- 8 | 3.95 | 157.82 | Pi/Cation |
| CG4 | CD2 | LEU- 23 | 4.5 | 0 | Hydrophobic |
| CE5 | CD2 | LEU- 23 | 4.32 | 0 | Hydrophobic |
| CD5 | CD2 | LEU- 23 | 3.78 | 0 | Hydrophobic |
| OA6 | OD1 | ASP- 25 | 3.39 | 127.35 | H-Bond (Ligand Donor) |
| CB3 | CB | ALA- 28 | 3.33 | 0 | Hydrophobic |
| O2 | N | ASP- 29 | 3.08 | 157.79 | H-Bond (Protein Donor) |
| N | O | GLY- 48 | 2.88 | 123.4 | H-Bond (Ligand Donor) |
| OA2 | N | ILE- 50 | 2.9 | 167.02 | H-Bond (Protein Donor) |
| CB3 | CD1 | ILE- 50 | 3.7 | 0 | Hydrophobic |
| CG3 | CG1 | ILE- 50 | 4.43 | 0 | Hydrophobic |
| CG4 | CG | PRO- 81 | 4.49 | 0 | Hydrophobic |
| CE4 | CG2 | VAL- 82 | 4.5 | 0 | Hydrophobic |
| CG4 | CG2 | VAL- 82 | 4.39 | 0 | Hydrophobic |
| CD4 | CG1 | VAL- 82 | 3.86 | 0 | Hydrophobic |
| CD5 | CD1 | ILE- 84 | 4.39 | 0 | Hydrophobic |
| CG3 | CD1 | ILE- 84 | 3.46 | 0 | Hydrophobic |
| CD3 | CD1 | ILE- 84 | 3.96 | 0 | Hydrophobic |
