sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-02-15
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1Z2 |
| AC: | P12499 |
| Organism: | Human immunodeficiency virus type 1 group M subtype D |
| Reign: | Viruses |
| TaxID: | 11683 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 50 % |
| B | 50 % |
| B-Factor: | 25.971 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.639 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 36.63 | 63.37 |
| According to VolSite | |
| HET Code: | 017 |
|---|---|
| Formula: | C27H37N3O7S |
| Molecular weight: | 547.664 g/mol |
| DrugBank ID: | DB01264 |
| Buried Surface Area: | 74.05 % |
| Polar Surface area: | 148.79 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: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -5.46905 | -0.844711 | -12.9666 |
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 | 3.92 | 0 | Hydrophobic |
| C37 | CD2 | LEU- 23 | 3.93 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.5 | 164.68 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.9 | 121.24 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.52 | 171.11 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.13 | 159.96 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.34 | 0 | Hydrophobic |
| C3 | CB | ALA- 28 | 3.53 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.9 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 3.97 | 0 | Hydrophobic |
| C29 | CB | ASP- 29 | 4.4 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 3.02 | 154.75 | H-Bond (Protein Donor) |
| N1 | O | ASP- 30 | 3.1 | 155.22 | H-Bond (Ligand Donor) |
| C25 | CB | ASP- 30 | 4.2 | 0 | Hydrophobic |
| C27 | CB | ASP- 30 | 4.43 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.05 | 154.04 | H-Bond (Protein Donor) |
| C25 | CG2 | VAL- 32 | 4.15 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 32 | 3.99 | 0 | Hydrophobic |
| C7 | CB | ILE- 47 | 4.08 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 47 | 4.36 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 3.97 | 0 | Hydrophobic |
| C33 | CB | ILE- 50 | 4.31 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.06 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 3.94 | 0 | Hydrophobic |
| C14 | CG | PRO- 81 | 4.23 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 4.09 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.49 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.97 | 0 | Hydrophobic |
| C36 | CG2 | VAL- 82 | 3.86 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 84 | 4.48 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 4.02 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 3.95 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.14 | 0 | Hydrophobic |
