sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2012-12-04
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1LW |
| AC: | P0C6F2 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 82834 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 53 % |
| B | 47 % |
| B-Factor: | 27.695 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.066 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.91 | 60.09 |
| According to VolSite | |
| HET Code: | G08 |
|---|---|
| Formula: | C28H37N3O8S |
| Molecular weight: | 575.674 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.39 % |
| Polar Surface area: | 165.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -18.2286 | 0.7533 | -0.00225 |
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 |
| C37 | CD2 | LEU- 23 | 3.98 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 23 | 3.64 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.9 | 158.33 | H-Bond (Protein Donor) |
| O18 | OD1 | ASP- 25 | 2.57 | 130.09 | H-Bond (Ligand Donor) |
| N20 | O | GLY- 27 | 3.34 | 140.62 | H-Bond (Ligand Donor) |
| C25 | CB | ALA- 28 | 4.02 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 3.96 | 0 | Hydrophobic |
| C6 | CB | ALA- 28 | 3.39 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 3.07 | 170.27 | H-Bond (Protein Donor) |
| O26 | N | ASP- 29 | 3.26 | 128.07 | H-Bond (Protein Donor) |
| C27 | CB | ASP- 29 | 4.29 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 32 | 3.87 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.81 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 47 | 4.34 | 0 | Hydrophobic |
| C3 | CB | ILE- 47 | 4.36 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.28 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 4.29 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.31 | 0 | Hydrophobic |
| C37 | CB | VAL- 82 | 4.29 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 82 | 3.57 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 82 | 3.48 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.67 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 84 | 3.83 | 0 | Hydrophobic |
| O22 | O | HOH- 239 | 3.05 | 180 | H-Bond (Protein Donor) |
