sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 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 | 93 % |
| B | 7 % |
| B-Factor: | 42.001 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.354 | 462.375 |
| % Hydrophobic | % Polar |
|---|---|
| 71.53 | 28.47 |
| According to VolSite | |
| HET Code: | PNU |
|---|---|
| Formula: | C13H11ClN4OS |
| Molecular weight: | 306.771 g/mol |
| DrugBank ID: | DB08414 |
| Buried Surface Area: | 76.38 % |
| Polar Surface area: | 103.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -10.3966 | 141.925 | 174.646 |
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 |
| C4 | CD2 | LEU- 100 | 4.39 | 0 | Hydrophobic |
| S17 | CG | LEU- 100 | 4.47 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 100 | 4.11 | 0 | Hydrophobic |
| N18 | O | LYS- 101 | 2.96 | 149.86 | H-Bond (Ligand Donor) |
| N2 | ND2 | ASN- 103 | 3.28 | 139.81 | H-Bond (Protein Donor) |
| CL19 | CG2 | VAL- 106 | 3.94 | 0 | Hydrophobic |
| S17 | CG1 | VAL- 179 | 4.45 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 179 | 4.15 | 0 | Hydrophobic |
| C21 | CB | TYR- 181 | 3.94 | 0 | Hydrophobic |
| C11 | CB | TYR- 181 | 4.35 | 0 | Hydrophobic |
| C11 | CB | TYR- 188 | 3.74 | 0 | Hydrophobic |
| C21 | CB | TYR- 188 | 3.99 | 0 | Hydrophobic |
| CL19 | CD2 | PHE- 227 | 3.56 | 0 | Hydrophobic |
| CL19 | CB | LEU- 234 | 3.42 | 0 | Hydrophobic |
| N18 | O | PRO- 236 | 3.43 | 131.15 | H-Bond (Ligand Donor) |
