sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2001-05-07
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 85 % |
| B | 15 % |
| B-Factor: | 47.307 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.650 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 74.45 | 25.55 |
| According to VolSite | |
| HET Code: | MSD |
|---|---|
| Formula: | C19H18N4O3S |
| Molecular weight: | 382.436 g/mol |
| DrugBank ID: | DB08212 |
| Buried Surface Area: | 77.22 % |
| Polar Surface area: | 139.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -10.0013 | 142.542 | 173.709 |
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 |
| C18 | CB | PRO- 95 | 4.01 | 0 | Hydrophobic |
| C44 | CB | PRO- 95 | 3.87 | 0 | Hydrophobic |
| C44 | CD2 | LEU- 100 | 3.39 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 100 | 4.38 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 100 | 3.49 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 100 | 4.03 | 0 | Hydrophobic |
| N8 | O | LYS- 101 | 2.67 | 171.22 | H-Bond (Ligand Donor) |
| C6 | CB | ASN- 103 | 3.83 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 106 | 4.07 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 179 | 3.66 | 0 | Hydrophobic |
| C44 | CG | TYR- 181 | 4.1 | 0 | Hydrophobic |
| C16 | CB | TYR- 181 | 3.4 | 0 | Hydrophobic |
| C13 | CB | TYR- 188 | 4.26 | 0 | Hydrophobic |
| C25 | CE2 | TYR- 188 | 4.08 | 0 | Hydrophobic |
| C21 | CB | TYR- 188 | 3.75 | 0 | Hydrophobic |
| C25 | CD2 | TRP- 229 | 3.34 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 234 | 4.44 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 234 | 3.59 | 0 | Hydrophobic |
| C44 | CB | GLU- 1138 | 3.55 | 0 | Hydrophobic |
