sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.540 Å
X-ray
2013-03-01
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 9.265 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.073 | 914.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.17 | 56.83 |
| According to VolSite | |
| HET Code: | M8Y |
|---|---|
| Formula: | C36H50BrN5O6 |
| Molecular weight: | 728.716 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.86 % |
| Polar Surface area: | 149.09 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 12.763 | 22.4601 | 5.69827 |
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 |
| C9 | CD2 | LEU- 23 | 4.46 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 23 | 4.07 | 0 | Hydrophobic |
| C4 | CB | ALA- 28 | 3.86 | 0 | Hydrophobic |
| O6 | N | ASP- 29 | 2.88 | 174.92 | H-Bond (Protein Donor) |
| C5 | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| C35 | CG1 | VAL- 32 | 4.33 | 0 | Hydrophobic |
| C5 | CB | ILE- 47 | 4.1 | 0 | Hydrophobic |
| N5 | O | GLY- 48 | 2.86 | 169.05 | H-Bond (Ligand Donor) |
| C16 | CB | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 50 | 4.25 | 0 | Hydrophobic |
| BR1 | CB | PRO- 81 | 3.8 | 0 | Hydrophobic |
| C21 | CG | PRO- 81 | 3.7 | 0 | Hydrophobic |
| C24 | CG2 | THR- 82 | 3.86 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 84 | 4.17 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 84 | 4.32 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 123 | 3.39 | 0 | Hydrophobic |
| O1 | OD2 | ASP- 125 | 2.68 | 158.63 | H-Bond (Ligand Donor) |
| N3 | O | GLY- 127 | 3 | 163.33 | H-Bond (Ligand Donor) |
| C17 | CB | ALA- 128 | 3.91 | 0 | Hydrophobic |
| O4 | N | ASP- 129 | 2.94 | 168.04 | H-Bond (Protein Donor) |
| C19 | CB | ASP- 129 | 4.23 | 0 | Hydrophobic |
| C15 | CB | ASP- 130 | 4.49 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 147 | 4.1 | 0 | Hydrophobic |
| N4 | O | GLY- 148 | 2.96 | 169.48 | H-Bond (Ligand Donor) |
| C8 | CG1 | ILE- 150 | 4.29 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 150 | 4.44 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 150 | 3.81 | 0 | Hydrophobic |
| C35 | CG1 | ILE- 150 | 3.92 | 0 | Hydrophobic |
| BR1 | CZ | PHE- 153 | 4.27 | 0 | Hydrophobic |
| C30 | CG | PRO- 181 | 3.84 | 0 | Hydrophobic |
| C32 | CG2 | THR- 182 | 3.64 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 184 | 4.4 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 184 | 4.41 | 0 | Hydrophobic |
