sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
1994-10-19
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV2RO |
| AC: | P04584 |
| Organism: | Human immunodeficiency virus type 2 subtype A |
| Reign: | Viruses |
| TaxID: | 11720 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 17.258 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.389 | 820.125 |
| % Hydrophobic | % Polar |
|---|---|
| 55.56 | 44.44 |
| According to VolSite | |
| HET Code: | 0DO |
|---|---|
| Formula: | C35H47N4O6S |
| Molecular weight: | 651.836 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.42 % |
| Polar Surface area: | 147.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 51.6826 | 22.196 | 3.69974 |
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 | OD1 | ASP- 25 | 2.83 | 124.33 | H-Bond (Ligand Donor) |
| OXT | OD2 | ASP- 25 | 2.78 | 161.64 | H-Bond (Ligand Donor) |
| OXT | OD1 | ASP- 25 | 2.54 | 157.1 | H-Bond (Protein Donor) |
| C2'1 | CB | ALA- 28 | 4.05 | 0 | Hydrophobic |
| C3'1 | CB | ALA- 28 | 4.11 | 0 | Hydrophobic |
| CM6 | CB | ALA- 28 | 4 | 0 | Hydrophobic |
| C4' | CB | ASP- 29 | 3.48 | 0 | Hydrophobic |
| C5' | CB | ASP- 30 | 3.95 | 0 | Hydrophobic |
| CM6 | CG2 | ILE- 32 | 3.88 | 0 | Hydrophobic |
| C2'1 | CG2 | ILE- 32 | 4.47 | 0 | Hydrophobic |
| C3'1 | CG2 | ILE- 32 | 3.89 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 47 | 4.32 | 0 | Hydrophobic |
| C2'1 | CG1 | VAL- 47 | 4.3 | 0 | Hydrophobic |
| C4'1 | CG1 | VAL- 47 | 3.71 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 47 | 3.68 | 0 | Hydrophobic |
| C6' | CG2 | VAL- 47 | 3.6 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 50 | 4.33 | 0 | Hydrophobic |
| C3'1 | CG1 | ILE- 50 | 3.89 | 0 | Hydrophobic |
| C4'1 | CG1 | ILE- 50 | 3.72 | 0 | Hydrophobic |
| CD1 | CG1 | ILE- 50 | 3.65 | 0 | Hydrophobic |
| C5' | CE | MET- 76 | 4.43 | 0 | Hydrophobic |
| CZ | CG | PRO- 81 | 3.67 | 0 | Hydrophobic |
| C51 | CG | PRO- 81 | 3.5 | 0 | Hydrophobic |
| O2S | N | ILE- 82 | 3.49 | 123.68 | H-Bond (Protein Donor) |
| CE2 | CD1 | ILE- 82 | 3.52 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 82 | 3.63 | 0 | Hydrophobic |
| CM6 | CD1 | ILE- 84 | 4.43 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 84 | 3.83 | 0 | Hydrophobic |
| C3'1 | CD1 | ILE- 84 | 3.68 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 84 | 3.65 | 0 | Hydrophobic |
