sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2010-09-22
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 21.849 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.764 | 742.500 |
| % Hydrophobic | % Polar |
|---|---|
| 41.82 | 58.18 |
| According to VolSite | |
| HET Code: | 017 |
|---|---|
| Formula: | C27H37N3O7S |
| Molecular weight: | 547.664 g/mol |
| DrugBank ID: | DB01264 |
| Buried Surface Area: | 70.57 % |
| 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 |
|---|---|---|
| 19.7094 | 29.7163 | 13.8994 |
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 | 3.85 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 3.92 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 3 | 123.41 | H-Bond (Ligand Donor) |
| O18 | OD2 | ASP- 25 | 2.6 | 166.69 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.53 | 169.78 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.2 | 152.9 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.41 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.59 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.79 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 3.9 | 0 | Hydrophobic |
| C29 | CB | ASP- 29 | 4.39 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 2.92 | 159 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 30 | 4.25 | 0 | Hydrophobic |
| C27 | CB | ASP- 30 | 4.47 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.06 | 160.19 | H-Bond (Protein Donor) |
| C25 | CG2 | VAL- 32 | 3.87 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.49 | 0 | Hydrophobic |
| C3 | CB | ILE- 47 | 4.31 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.14 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 4.01 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.15 | 0 | Hydrophobic |
| C14 | CG | PRO- 81 | 4.26 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 4.31 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.78 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.83 | 0 | Hydrophobic |
| C34 | CG1 | VAL- 82 | 3.66 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.07 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 4.41 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 4.04 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 84 | 4.15 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
