sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2007-07-03
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1A2 |
| AC: | P03369 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11685 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 15.447 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.954 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 47.41 | 52.59 |
| According to VolSite | |
| HET Code: | MZ8 |
|---|---|
| Formula: | C28H31N3O5S2 |
| Molecular weight: | 553.693 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.34 % |
| Polar Surface area: | 156.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 19.387 | 30.6562 | 14.248 |
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 | 3.99 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 23 | 3.78 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.56 | 164.31 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.56 | 169.84 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.16 | 167.69 | H-Bond (Ligand Donor) |
| C7 | CB | ALA- 28 | 3.32 | 0 | Hydrophobic |
| C27 | CB | ALA- 28 | 4.01 | 0 | Hydrophobic |
| C25 | CB | ASP- 29 | 3.78 | 0 | Hydrophobic |
| N1 | N | ASP- 30 | 3.2 | 140.48 | H-Bond (Protein Donor) |
| C26 | CB | ASP- 30 | 4.41 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 30 | 2.78 | 167.25 | H-Bond (Ligand Donor) |
| C7 | CG2 | VAL- 32 | 3.88 | 0 | Hydrophobic |
| S1 | CB | ILE- 47 | 3.97 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.31 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 4.31 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 50 | 3.81 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.17 | 0 | Hydrophobic |
| C14 | CG | PRO- 81 | 4.33 | 0 | Hydrophobic |
| C35 | CG | PRO- 81 | 3.67 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 82 | 3.55 | 0 | Hydrophobic |
| C34 | CG2 | VAL- 82 | 3.27 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.43 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 4.48 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.09 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 84 | 3.96 | 0 | Hydrophobic |
