sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-09-20
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 14.353 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.015 | 803.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.18 | 58.82 |
| According to VolSite | |
| HET Code: | 1UN |
|---|---|
| Formula: | C32H46N3O4S |
| Molecular weight: | 568.790 g/mol |
| DrugBank ID: | DB00220 |
| Buried Surface Area: | 69.14 % |
| Polar Surface area: | 128.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 5.50408 | -1.84267 | 14.5379 |
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 |
| C1 | CD2 | LEU- 23 | 4.17 | 0 | Hydrophobic |
| C82 | CD2 | LEU- 23 | 3.95 | 0 | Hydrophobic |
| N7 | OD2 | ASP- 25 | 4 | 0 | Ionic (Ligand Cationic) |
| O21 | OD1 | ASP- 25 | 2.63 | 132.82 | H-Bond (Ligand Donor) |
| O21 | OD2 | ASP- 25 | 2.76 | 150.44 | H-Bond (Ligand Donor) |
| N22 | O | GLY- 27 | 3.29 | 164.97 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 4.08 | 0 | Hydrophobic |
| C39 | CB | ALA- 28 | 3.97 | 0 | Hydrophobic |
| C34 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| C32 | CB | ASP- 29 | 4 | 0 | Hydrophobic |
| C16 | CB | ASP- 30 | 3.9 | 0 | Hydrophobic |
| C33 | CB | ASP- 30 | 4.41 | 0 | Hydrophobic |
| O38 | OD2 | ASP- 30 | 3.16 | 156.84 | H-Bond (Ligand Donor) |
| C14 | CG2 | VAL- 32 | 3.91 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 32 | 4.3 | 0 | Hydrophobic |
| C39 | CG2 | VAL- 32 | 4.03 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 47 | 3.9 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 47 | 4.5 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.99 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 50 | 3.62 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 50 | 3.31 | 0 | Hydrophobic |
| C5 | CG | PRO- 81 | 4.23 | 0 | Hydrophobic |
| C4 | CG | PRO- 81 | 3.33 | 0 | Hydrophobic |
| C79 | CB | PRO- 81 | 3.61 | 0 | Hydrophobic |
| C3 | CB | THR- 82 | 4.01 | 0 | Hydrophobic |
| C81 | CG2 | THR- 82 | 3.39 | 0 | Hydrophobic |
| C82 | CG2 | VAL- 84 | 4.28 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 84 | 3.74 | 0 | Hydrophobic |
| S74 | CG2 | VAL- 84 | 4.09 | 0 | Hydrophobic |
