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
1999-10-04
| 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: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 50 % |
| B | 50 % |
| B-Factor: | 13.472 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.819 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.03 | 58.97 |
| According to VolSite | |
| HET Code: | PI9 |
|---|---|
| Formula: | C32H48N4O6S |
| Molecular weight: | 616.812 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.99 % |
| Polar Surface area: | 159.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 5.99033 | -0.498442 | 13.2366 |
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 | 4.19 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 23 | 3.79 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 25 | 2.75 | 154.76 | H-Bond (Protein Donor) |
| O4 | OD2 | ASP- 25 | 2.65 | 173.22 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 27 | 3.24 | 150.71 | H-Bond (Ligand Donor) |
| C21 | CB | ALA- 28 | 4.26 | 0 | Hydrophobic |
| C31 | CB | ALA- 28 | 3.49 | 0 | Hydrophobic |
| C10 | CB | ALA- 28 | 3.87 | 0 | Hydrophobic |
| C5 | CB | ASP- 29 | 4.45 | 0 | Hydrophobic |
| O1 | N | ASP- 29 | 2.76 | 167.07 | H-Bond (Protein Donor) |
| C9 | CG2 | VAL- 32 | 3.96 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 32 | 4.39 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 47 | 4.47 | 0 | Hydrophobic |
| C29 | CB | ILE- 47 | 4.14 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 47 | 4.09 | 0 | Hydrophobic |
| N1 | O | GLY- 48 | 2.98 | 168.17 | H-Bond (Ligand Donor) |
| C25 | CG1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 50 | 3.3 | 0 | Hydrophobic |
| C18 | CG | PRO- 81 | 4.41 | 0 | Hydrophobic |
| C1 | CB | PRO- 81 | 3.77 | 0 | Hydrophobic |
| C25 | CG | PRO- 81 | 3.56 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 82 | 3.28 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 82 | 3.69 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 84 | 3.53 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 4.07 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 84 | 3.8 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 3.4 | 0 | Hydrophobic |
