sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
1999-07-21
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1H2 |
| AC: | P04585 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11706 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 32.530 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.666 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 67.86 | 32.14 |
| According to VolSite | |
| HET Code: | 612 |
|---|---|
| Formula: | C16H26N2O3S |
| Molecular weight: | 326.454 g/mol |
| DrugBank ID: | DB07184 |
| Buried Surface Area: | 75.07 % |
| Polar Surface area: | 83.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -2.14877 | -33.8282 | 24.5827 |
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 |
| C5 | CG | PRO- 95 | 4.08 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 100 | 4.11 | 0 | Hydrophobic |
| CI | CD2 | LEU- 100 | 4.15 | 0 | Hydrophobic |
| CA | CD1 | LEU- 100 | 4.09 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 100 | 3.8 | 0 | Hydrophobic |
| N10 | O | LYS- 101 | 2.58 | 169.6 | H-Bond (Ligand Donor) |
| S | CG1 | VAL- 106 | 3.75 | 0 | Hydrophobic |
| CF | CG2 | VAL- 106 | 4.37 | 0 | Hydrophobic |
| CH | CG1 | VAL- 106 | 3.47 | 0 | Hydrophobic |
| CC | CG2 | VAL- 106 | 4.13 | 0 | Hydrophobic |
| CD | CB | VAL- 106 | 4 | 0 | Hydrophobic |
| CI | CB | TYR- 181 | 3.74 | 0 | Hydrophobic |
| C5 | CD1 | TYR- 181 | 3.86 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 188 | 4.18 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 188 | 4.43 | 0 | Hydrophobic |
| C6 | CG | TYR- 188 | 4.38 | 0 | Hydrophobic |
| S | CB | TYR- 188 | 3.88 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 188 | 3.51 | 0 | Hydrophobic |
| CH | CB | TYR- 188 | 3.6 | 0 | Hydrophobic |
| CD | CG | PRO- 225 | 3.89 | 0 | Hydrophobic |
| S | CD2 | PHE- 227 | 4.32 | 0 | Hydrophobic |
| CC | CD2 | PHE- 227 | 4.13 | 0 | Hydrophobic |
| CD | CE2 | PHE- 227 | 3.63 | 0 | Hydrophobic |
| C2 | CB | PHE- 227 | 4.06 | 0 | Hydrophobic |
| C5 | CE2 | TRP- 229 | 4.29 | 0 | Hydrophobic |
| C4 | CD2 | TRP- 229 | 3.46 | 0 | Hydrophobic |
| CA | CB | LEU- 234 | 3.81 | 0 | Hydrophobic |
| CC | CB | LEU- 234 | 4.47 | 0 | Hydrophobic |
| CD | CB | PRO- 236 | 4.42 | 0 | Hydrophobic |
| CA | CZ | TYR- 318 | 4.23 | 0 | Hydrophobic |
| O11 | O | HOH- 1001 | 3.03 | 161.4 | H-Bond (Protein Donor) |
