sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2005-10-17
| 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 | 50 % |
| B | 50 % |
| B-Factor: | 13.377 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.850 | 776.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.48 | 56.52 |
| According to VolSite | |
| HET Code: | AKC |
|---|---|
| Formula: | C36H40N3O7 |
| Molecular weight: | 626.719 g/mol |
| DrugBank ID: | DB04623 |
| Buried Surface Area: | 68.58 % |
| Polar Surface area: | 139.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 17.4881 | 19.4002 | 5.67945 |
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 |
| C42 | CD2 | LEU- 23 | 3.8 | 0 | Hydrophobic |
| O07 | OD2 | ASP- 25 | 3.3 | 122.81 | H-Bond (Ligand Donor) |
| O07 | OD1 | ASP- 25 | 2.52 | 151.8 | H-Bond (Ligand Donor) |
| C27 | CB | ALA- 28 | 3.65 | 0 | Hydrophobic |
| O52 | N | ASP- 29 | 2.87 | 150.27 | H-Bond (Protein Donor) |
| C24 | CB | ASP- 30 | 4 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 32 | 3.59 | 0 | Hydrophobic |
| C23 | CB | ILE- 47 | 4.39 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 47 | 3.97 | 0 | Hydrophobic |
| C48 | CG1 | ILE- 50 | 4.38 | 0 | Hydrophobic |
| C39 | CB | PRO- 81 | 3.9 | 0 | Hydrophobic |
| C41 | CG1 | VAL- 82 | 3.72 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 84 | 3.97 | 0 | Hydrophobic |
| C36 | CD1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 223 | 3.4 | 0 | Hydrophobic |
| O07 | OD2 | ASP- 225 | 2.62 | 170.46 | H-Bond (Protein Donor) |
| N29 | OD1 | ASP- 225 | 3.02 | 140.27 | H-Bond (Ligand Donor) |
| NP4 | O | GLY- 227 | 3.26 | 163.53 | H-Bond (Ligand Donor) |
| C48 | CB | ALA- 228 | 3.59 | 0 | Hydrophobic |
| O46 | N | ASP- 230 | 3.21 | 150.03 | H-Bond (Protein Donor) |
| C47 | CB | ASP- 230 | 4.16 | 0 | Hydrophobic |
| C47 | CG2 | VAL- 232 | 3.34 | 0 | Hydrophobic |
| C45 | CB | ILE- 247 | 4.19 | 0 | Hydrophobic |
| C47 | CD1 | ILE- 247 | 4.21 | 0 | Hydrophobic |
| C15 | CB | PRO- 281 | 3.58 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 282 | 4.18 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 282 | 3.68 | 0 | Hydrophobic |
| C48 | CD1 | ILE- 284 | 4.27 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 284 | 3.3 | 0 | Hydrophobic |
