sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2011-11-01
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1Y2 |
| AC: | P35963 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 362651 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 47 % |
| B | 53 % |
| B-Factor: | 14.214 |
|---|---|
| Number of residues: | 48 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.197 | 907.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.84 | 53.16 |
| According to VolSite | |
| HET Code: | QG8 |
|---|---|
| Formula: | C44H52N4O6 |
| Molecular weight: | 732.907 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.6 % |
| Polar Surface area: | 131.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 13.5292 | 22.2125 | 6.5968 |
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 |
| C35 | CD2 | LEU- 23 | 4.09 | 0 | Hydrophobic |
| O17 | OD2 | ASP- 25 | 2.7 | 141.62 | H-Bond (Ligand Donor) |
| C4 | CB | ALA- 28 | 4.22 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 3.81 | 0 | Hydrophobic |
| C14 | CB | ASP- 29 | 4.36 | 0 | Hydrophobic |
| C14 | CB | ASP- 30 | 4.08 | 0 | Hydrophobic |
| C9 | CB | ILE- 47 | 3.97 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 47 | 3.73 | 0 | Hydrophobic |
| C46 | CG1 | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 76 | 3.76 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.51 | 0 | Hydrophobic |
| C50 | CB | PRO- 81 | 3.66 | 0 | Hydrophobic |
| C32 | CG2 | THR- 82 | 3.42 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 84 | 4.31 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 123 | 3.34 | 0 | Hydrophobic |
| N37 | O | GLY- 127 | 3.16 | 140.37 | H-Bond (Ligand Donor) |
| C46 | CB | ALA- 128 | 3.94 | 0 | Hydrophobic |
| C43 | CB | ASP- 129 | 4.41 | 0 | Hydrophobic |
| O44 | N | ASP- 129 | 2.87 | 160.49 | H-Bond (Protein Donor) |
| C47 | CB | ASP- 130 | 4.37 | 0 | Hydrophobic |
| C46 | CG1 | VAL- 132 | 4.42 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 147 | 3.7 | 0 | Hydrophobic |
| C47 | CD1 | ILE- 147 | 4.14 | 0 | Hydrophobic |
| N40 | O | GLY- 148 | 3.13 | 161.35 | H-Bond (Ligand Donor) |
| C20 | CG1 | ILE- 150 | 3.95 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 150 | 3.91 | 0 | Hydrophobic |
| C26 | CG | PRO- 181 | 3.28 | 0 | Hydrophobic |
| C25 | CB | THR- 182 | 3.52 | 0 | Hydrophobic |
| C46 | CG2 | VAL- 184 | 4.27 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 184 | 3.55 | 0 | Hydrophobic |
| O12 | O | HOH- 2029 | 2.78 | 164.84 | H-Bond (Protein Donor) |
