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 | 45 % |
| B | 55 % |
| B-Factor: | 20.199 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.963 | 708.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.76 | 55.24 |
| According to VolSite | |
| HET Code: | MZ1 |
|---|---|
| Formula: | C26H28F3N3O5S2 |
| Molecular weight: | 583.643 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.04 % |
| Polar Surface area: | 152.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 19.3634 | 30.8786 | 14.3362 |
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 |
| C32 | CD2 | LEU- 23 | 4.44 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 4.14 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.6 | 173.06 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.58 | 164.37 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.09 | 147.59 | H-Bond (Ligand Donor) |
| C23 | CB | ALA- 28 | 4.11 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 4.26 | 0 | Hydrophobic |
| C4 | CB | ALA- 28 | 3.66 | 0 | Hydrophobic |
| O26 | N | ASP- 29 | 2.85 | 173.79 | H-Bond (Protein Donor) |
| F2 | CB | ASP- 30 | 3.36 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 32 | 4.45 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 32 | 4.17 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 32 | 3.62 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.23 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 47 | 4.09 | 0 | Hydrophobic |
| F1 | CB | ILE- 47 | 3.4 | 0 | Hydrophobic |
| N24 | O | GLY- 48 | 2.91 | 157.09 | H-Bond (Ligand Donor) |
| C23 | CD1 | ILE- 50 | 3.67 | 0 | Hydrophobic |
| S1 | CG1 | ILE- 50 | 4.34 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| F2 | CD1 | LEU- 76 | 4.2 | 0 | Hydrophobic |
| S1 | CG | PRO- 81 | 4.36 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.6 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 82 | 3.58 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 84 | 3.83 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 84 | 4.45 | 0 | Hydrophobic |
| F3 | CG2 | ILE- 84 | 3.45 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
