sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.480 Å
X-ray
2007-07-19
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 12.935 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.793 | 877.500 |
| % Hydrophobic | % Polar |
|---|---|
| 41.92 | 58.08 |
| According to VolSite | |
| HET Code: | QN1 |
|---|---|
| Formula: | C34H32F6N5O6S2 |
| Molecular weight: | 784.768 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.57 % |
| Polar Surface area: | 194.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 11.8155 | -19.9421 | -17.2196 |
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 |
| F3 | CD | ARG- 8 | 4.32 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 23 | 3.9 | 0 | Hydrophobic |
| C30 | CD2 | LEU- 23 | 3.57 | 0 | Hydrophobic |
| N22 | OD2 | ASP- 25 | 2.97 | 129.04 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 25 | 2.79 | 164.28 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 25 | 2.67 | 154.93 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 25 | 2.97 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 25 | 2.79 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 25 | 2.87 | 0 | Ionic (Ligand Cationic) |
| N22 | OD2 | ASP- 25 | 2.67 | 0 | Ionic (Ligand Cationic) |
| C18 | CB | ALA- 28 | 3.63 | 0 | Hydrophobic |
| C1 | CB | ALA- 28 | 3.86 | 0 | Hydrophobic |
| O1 | N | ASP- 30 | 2.84 | 145.97 | H-Bond (Protein Donor) |
| O2 | N | ASP- 30 | 3.05 | 137.45 | H-Bond (Protein Donor) |
| N2 | OD1 | ASP- 30 | 2.93 | 155.21 | H-Bond (Ligand Donor) |
| C1 | CG2 | VAL- 32 | 3.95 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 32 | 3.89 | 0 | Hydrophobic |
| C5 | CB | ILE- 47 | 4.09 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 47 | 4.16 | 0 | Hydrophobic |
| C35 | CB | ILE- 50 | 4.28 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 50 | 3.3 | 0 | Hydrophobic |
| O41 | N | ILE- 50 | 2.94 | 170 | H-Bond (Protein Donor) |
| O10 | N | ILE- 50 | 3.05 | 145.96 | H-Bond (Protein Donor) |
| C36 | CG | PRO- 81 | 4.13 | 0 | Hydrophobic |
| F2 | CB | PRO- 81 | 3.77 | 0 | Hydrophobic |
| F4 | CG | PRO- 81 | 3.32 | 0 | Hydrophobic |
| C29 | CG | PRO- 81 | 3.69 | 0 | Hydrophobic |
| F2 | CG1 | VAL- 82 | 4.28 | 0 | Hydrophobic |
| F4 | CG1 | VAL- 82 | 3.41 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 82 | 4.05 | 0 | Hydrophobic |
| C37 | CG1 | VAL- 82 | 3.79 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 84 | 3.5 | 0 | Hydrophobic |
| C38 | CD1 | ILE- 84 | 3.3 | 0 | Hydrophobic |
