sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1996-12-10
| 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 | 43 % |
| B | 57 % |
| B-Factor: | 17.134 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.963 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.68 | 57.32 |
| According to VolSite | |
| HET Code: | UNI |
|---|---|
| Formula: | C28H27N2O5S |
| Molecular weight: | 503.589 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.42 % |
| Polar Surface area: | 127.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 15.4442 | 21.7714 | 5.81292 |
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 |
| CZ5 | CD | ARG- 8 | 4.09 | 0 | Hydrophobic |
| CG4 | CD2 | LEU- 23 | 3.97 | 0 | Hydrophobic |
| CZ5 | CD2 | LEU- 23 | 4.21 | 0 | Hydrophobic |
| CD5 | CD2 | LEU- 23 | 3.88 | 0 | Hydrophobic |
| OA6 | OD1 | ASP- 25 | 3.03 | 120.24 | H-Bond (Ligand Donor) |
| CD6 | CB | ALA- 28 | 4.13 | 0 | Hydrophobic |
| CB3 | CB | ALA- 28 | 3.37 | 0 | Hydrophobic |
| O2 | N | ASP- 29 | 3.2 | 157.66 | H-Bond (Protein Donor) |
| CB3 | CG2 | VAL- 32 | 4.13 | 0 | Hydrophobic |
| CB4 | CD1 | ILE- 47 | 4.32 | 0 | Hydrophobic |
| OA2 | N | ILE- 50 | 2.99 | 139.68 | H-Bond (Protein Donor) |
| CG3 | CG2 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 50 | 4.42 | 0 | Hydrophobic |
| CD3 | CG1 | ILE- 50 | 4.45 | 0 | Hydrophobic |
| CB2 | CG1 | ILE- 50 | 4.2 | 0 | Hydrophobic |
| CG3 | CG1 | VAL- 82 | 3.77 | 0 | Hydrophobic |
| CD4 | CG2 | VAL- 82 | 4.42 | 0 | Hydrophobic |
| CG3 | CD1 | ILE- 84 | 3.22 | 0 | Hydrophobic |
| CD4 | CD1 | ILE- 84 | 3.39 | 0 | Hydrophobic |
