sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.290 Å
X-ray
2012-10-02
| 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 | 50 % |
| B | 50 % |
| B-Factor: | 11.850 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.012 | 995.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.32 | 60.68 |
| According to VolSite | |
| HET Code: | G52 |
|---|---|
| Formula: | C30H40N2O9S |
| Molecular weight: | 604.712 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.69 % |
| Polar Surface area: | 141.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 11.89 | -19.9338 | -18.3615 |
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 |
| C15 | CD2 | LEU- 23 | 3.82 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 3.86 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.56 | 151.07 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.6 | 120.2 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.73 | 152.28 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.26 | 164.47 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.06 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.94 | 0 | Hydrophobic |
| C4 | CB | ALA- 28 | 3.4 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 3.94 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 3.9 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 2.91 | 171.34 | H-Bond (Protein Donor) |
| C2 | CB | ASP- 30 | 4.29 | 0 | Hydrophobic |
| C40 | CB | ASP- 30 | 3.75 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.3 | 159.04 | H-Bond (Protein Donor) |
| O39 | N | ASP- 30 | 3.21 | 129.32 | H-Bond (Protein Donor) |
| C25 | CG2 | VAL- 32 | 4.1 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 32 | 4 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.45 | 0 | Hydrophobic |
| C7 | CB | ILE- 47 | 4.37 | 0 | Hydrophobic |
| C40 | CG2 | ILE- 47 | 4.04 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 3.85 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 4.21 | 0 | Hydrophobic |
| C35 | CB | PRO- 81 | 3.94 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.77 | 0 | Hydrophobic |
| C15 | CB | ALA- 82 | 4.03 | 0 | Hydrophobic |
| C34 | CB | ALA- 82 | 3.84 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 84 | 4.38 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 3.33 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.78 | 0 | Hydrophobic |
| C32 | CG2 | ILE- 84 | 4.2 | 0 | Hydrophobic |
