sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2009-07-08
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 21.140 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.941 | 772.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.36 | 57.64 |
| According to VolSite | |
| HET Code: | DJR |
|---|---|
| Formula: | C28H38N2O8S |
| Molecular weight: | 562.675 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.25 % |
| Polar Surface area: | 132.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 5.78354 | -1.14713 | 14.2918 |
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 |
| C10 | CD1 | LEU- 23 | 4.19 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 23 | 4.4 | 0 | Hydrophobic |
| O6 | OD1 | ASP- 25 | 2.56 | 168 | H-Bond (Protein Donor) |
| N1 | O | GLY- 27 | 3.28 | 155.41 | H-Bond (Ligand Donor) |
| C15 | CB | ALA- 28 | 4.39 | 0 | Hydrophobic |
| C3 | CB | ALA- 28 | 3.77 | 0 | Hydrophobic |
| C23 | CB | ALA- 28 | 3.63 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 3.99 | 0 | Hydrophobic |
| C2 | CB | ASP- 29 | 4.41 | 0 | Hydrophobic |
| C26 | CB | ASP- 29 | 4.1 | 0 | Hydrophobic |
| O9 | N | ASP- 29 | 2.96 | 159.55 | H-Bond (Protein Donor) |
| O | N | ASP- 30 | 2.9 | 161.14 | H-Bond (Protein Donor) |
| O1 | N | ASP- 30 | 3.41 | 141.21 | H-Bond (Protein Donor) |
| C27 | CB | ASP- 30 | 4.47 | 0 | Hydrophobic |
| C3 | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| C26 | CB | ASP- 30 | 3.96 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 32 | 4.02 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 32 | 3.85 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 47 | 4.33 | 0 | Hydrophobic |
| C26 | CG2 | ILE- 47 | 3.85 | 0 | Hydrophobic |
| C20 | CB | ILE- 47 | 4.25 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.03 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 50 | 3.54 | 0 | Hydrophobic |
| C14 | CG | PRO- 81 | 3.82 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 82 | 3.62 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 82 | 3.77 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 84 | 3.59 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 84 | 4.04 | 0 | Hydrophobic |
