sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.220 Å
X-ray
2011-07-21
| 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 | 35 % |
| B | 65 % |
| B-Factor: | 24.386 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 1.306 | 1123.875 |
| % Hydrophobic | % Polar |
|---|---|
| 43.84 | 56.16 |
| According to VolSite | |
| HET Code: | 3T1 |
|---|---|
| Formula: | C26H23ClN2O3 |
| Molecular weight: | 446.925 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.36 % |
| Polar Surface area: | 70.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 1.49303 | 1.18787 | 19.2178 |
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 |
| C24 | CD | ARG- 8 | 3.95 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 23 | 3.65 | 0 | Hydrophobic |
| N10 | O | GLY- 27 | 3.02 | 123.6 | H-Bond (Ligand Donor) |
| C17 | CG2 | VAL- 32 | 4.23 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 32 | 3.93 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 47 | 3.46 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 50 | 4.42 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 50 | 4 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 3.46 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 50 | 3.77 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 54 | 3.9 | 0 | Hydrophobic |
| C16 | CB | THR- 80 | 3.7 | 0 | Hydrophobic |
| C21 | CB | PRO- 81 | 4.17 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.89 | 0 | Hydrophobic |
| CL1 | CG | PRO- 81 | 3.81 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 82 | 3.84 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 82 | 3.54 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 82 | 3.89 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 84 | 3.93 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 84 | 4.28 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 84 | 3.75 | 0 | Hydrophobic |
