sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
1997-04-17
| 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: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 53 % |
| B | 47 % |
| B-Factor: | 17.854 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL CL |
| Ligandability | Volume (Å3) |
|---|---|
| 1.164 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.01 | 52.99 |
| According to VolSite | |
| HET Code: | THK |
|---|---|
| Formula: | C23H28ClFNOS2 |
| Molecular weight: | 453.056 g/mol |
| DrugBank ID: | DB08622 |
| Buried Surface Area: | 47.93 % |
| Polar Surface area: | 75.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 5.08841 | -0.137448 | 13.167 |
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 |
| C9 | CD2 | LEU- 23 | 3.81 | 0 | Hydrophobic |
| S58 | CD2 | LEU- 23 | 4.27 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 23 | 3.91 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 25 | 3.83 | 0 | Ionic (Ligand Cationic) |
| O19 | OD2 | ASP- 25 | 2.89 | 170.59 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 28 | 4.32 | 0 | Hydrophobic |
| F18 | CB | ALA- 28 | 4.4 | 0 | Hydrophobic |
| F18 | CB | ASP- 29 | 4.05 | 0 | Hydrophobic |
| F18 | CB | ASP- 30 | 4.49 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 50 | 4.24 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 50 | 4.18 | 0 | Hydrophobic |
| CL6 | CG | PRO- 81 | 3.55 | 0 | Hydrophobic |
| C52 | CG | PRO- 81 | 4.3 | 0 | Hydrophobic |
| C22 | CG | PRO- 81 | 3.78 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 82 | 4.3 | 0 | Hydrophobic |
| C52 | CG2 | VAL- 82 | 4.18 | 0 | Hydrophobic |
| S58 | CG2 | VAL- 82 | 3.83 | 0 | Hydrophobic |
| CL6 | CG1 | VAL- 82 | 3.59 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 84 | 4.48 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 84 | 4.46 | 0 | Hydrophobic |
