sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.970 Å
X-ray
1999-10-06
| 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 | 55 % |
| B | 45 % |
| B-Factor: | 22.791 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.922 | 803.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.80 | 54.20 |
| According to VolSite | |
| HET Code: | TPV |
|---|---|
| Formula: | C31H32F3N2O5S |
| Molecular weight: | 601.656 g/mol |
| DrugBank ID: | DB00932 |
| Buried Surface Area: | 64.81 % |
| Polar Surface area: | 116.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 11.6867 | 24.3403 | 5.74588 |
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 |
| F40 | CD | ARG- 8 | 3.59 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 23 | 3.65 | 0 | Hydrophobic |
| F40 | CD2 | LEU- 23 | 3.43 | 0 | Hydrophobic |
| O8 | OD2 | ASP- 25 | 3.37 | 164.3 | H-Bond (Ligand Donor) |
| O8 | OD2 | ASP- 25 | 3.24 | 124.08 | H-Bond (Ligand Donor) |
| C11 | CB | ALA- 28 | 3.9 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 3.6 | 0 | Hydrophobic |
| O31 | N | ASP- 29 | 3.4 | 130.31 | H-Bond (Protein Donor) |
| N34 | N | ASP- 29 | 3.4 | 161.18 | H-Bond (Protein Donor) |
| O31 | N | ASP- 30 | 3.28 | 146.73 | H-Bond (Protein Donor) |
| C11 | CG2 | VAL- 32 | 4.35 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 32 | 4.01 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 47 | 4.43 | 0 | Hydrophobic |
| C26 | CD1 | ILE- 47 | 4.29 | 0 | Hydrophobic |
| O7 | N | ILE- 50 | 2.99 | 163.88 | H-Bond (Protein Donor) |
| O7 | N | ILE- 50 | 2.97 | 166 | H-Bond (Protein Donor) |
| C11 | CG1 | ILE- 50 | 4.12 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 50 | 4.38 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 4.09 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 82 | 4.26 | 0 | Hydrophobic |
| F41 | CG1 | VAL- 82 | 3.87 | 0 | Hydrophobic |
| F42 | CG2 | VAL- 82 | 4.03 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 82 | 3.47 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.63 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 4.12 | 0 | Hydrophobic |
