sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
0.880 Å
X-ray
2009-05-26
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 7.204 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.974 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.24 | 56.76 |
| According to VolSite | |
| HET Code: | KNJ |
|---|---|
| Formula: | C30H40N4O5S |
| Molecular weight: | 568.727 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.98 % |
| Polar Surface area: | 159.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 15.4973 | 21.5884 | 17.6868 |
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 |
| C18 | CD2 | LEU- 23 | 4.33 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 25 | 2.67 | 153.55 | H-Bond (Protein Donor) |
| C30 | CB | ALA- 28 | 3.75 | 0 | Hydrophobic |
| C30 | CG2 | VAL- 32 | 4.23 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 50 | 4.21 | 0 | Hydrophobic |
| S2 | CG1 | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C15 | CG | PRO- 81 | 3.89 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 82 | 3.51 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 84 | 3.77 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 84 | 3.88 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.81 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 123 | 3.36 | 0 | Hydrophobic |
| O2 | OD1 | ASP- 125 | 2.64 | 160.65 | H-Bond (Ligand Donor) |
| O2 | OD2 | ASP- 125 | 3.14 | 130.7 | H-Bond (Ligand Donor) |
| N3 | O | GLY- 127 | 3.49 | 152.73 | H-Bond (Ligand Donor) |
| C1 | CB | ALA- 128 | 4.05 | 0 | Hydrophobic |
| C8 | CB | ALA- 128 | 4.39 | 0 | Hydrophobic |
| C4 | CB | ASP- 129 | 3.58 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 130 | 3.02 | 142.78 | H-Bond (Ligand Donor) |
| C3 | CB | ASP- 130 | 3.68 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 132 | 3.54 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 147 | 3.89 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 147 | 3.61 | 0 | Hydrophobic |
| C14 | CB | ILE- 150 | 4.35 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 150 | 4.19 | 0 | Hydrophobic |
| C23 | CG | PRO- 181 | 4.39 | 0 | Hydrophobic |
| S2 | CG | PRO- 181 | 3.81 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 182 | 3.75 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 184 | 4.34 | 0 | Hydrophobic |
| S2 | CD1 | ILE- 184 | 3.74 | 0 | Hydrophobic |
