sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.810 Å
X-ray
2007-08-29
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B5 |
| AC: | P04587 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11682 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 50 % |
| B | 50 % |
| B-Factor: | 20.447 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.819 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 41.81 | 58.19 |
| According to VolSite | |
| HET Code: | G4G |
|---|---|
| Formula: | C32H34N5O6S2 |
| Molecular weight: | 648.772 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.23 % |
| Polar Surface area: | 194.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 11.836 | -20.0502 | -17.5756 |
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 |
| C30 | CD2 | LEU- 23 | 3.89 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 23 | 3.7 | 0 | Hydrophobic |
| N22 | OD2 | ASP- 25 | 2.88 | 133.62 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 25 | 2.82 | 148.59 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 25 | 2.69 | 154.99 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 25 | 2.88 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 25 | 2.82 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 25 | 2.94 | 0 | Ionic (Ligand Cationic) |
| N22 | OD2 | ASP- 25 | 2.69 | 0 | Ionic (Ligand Cationic) |
| C17 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| C2 | CB | ALA- 28 | 3.74 | 0 | Hydrophobic |
| O2 | N | ASP- 30 | 2.87 | 145.22 | H-Bond (Protein Donor) |
| O1 | N | ASP- 30 | 3 | 138.14 | H-Bond (Protein Donor) |
| N1 | OD1 | ASP- 30 | 3.1 | 157.28 | H-Bond (Ligand Donor) |
| C1 | CG2 | VAL- 32 | 3.63 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 32 | 3.78 | 0 | Hydrophobic |
| C3 | CB | ILE- 47 | 4.33 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 47 | 4.4 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 47 | 4.12 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 50 | 4.17 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 50 | 3.55 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 50 | 3.78 | 0 | Hydrophobic |
| O40 | N | ILE- 50 | 3.19 | 159.34 | H-Bond (Protein Donor) |
| C35 | CG | PRO- 81 | 3.61 | 0 | Hydrophobic |
| C39 | CG1 | VAL- 82 | 4.01 | 0 | Hydrophobic |
| C31 | CG1 | VAL- 82 | 3.42 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 84 | 4.1 | 0 | Hydrophobic |
| C38 | CG1 | VAL- 84 | 4.23 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 84 | 4.06 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 84 | 3.79 | 0 | Hydrophobic |
