sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.510 Å
X-ray
2012-07-11
| 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: | 33.843 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.589 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 70.30 | 29.70 |
| According to VolSite | |
| HET Code: | T27 |
|---|---|
| Formula: | C22H18N6 |
| Molecular weight: | 366.419 g/mol |
| DrugBank ID: | DB08864 |
| Buried Surface Area: | 77.83 % |
| Polar Surface area: | 97.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 49.8266 | -27.4093 | 36.9004 |
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 |
| C7 | CG | PRO- 95 | 3.86 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 100 | 3.87 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 100 | 4 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 100 | 4.17 | 0 | Hydrophobic |
| N2 | N | LYS- 101 | 3.24 | 166.61 | H-Bond (Protein Donor) |
| N4 | O | LYS- 101 | 2.81 | 157.43 | H-Bond (Ligand Donor) |
| C14 | CB | LYS- 103 | 4.39 | 0 | Hydrophobic |
| C15 | CG | LYS- 103 | 3.71 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 106 | 4.3 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 106 | 3.87 | 0 | Hydrophobic |
| C10 | CG | GLU- 138 | 4.22 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 179 | 3.9 | 0 | Hydrophobic |
| C10 | CB | VAL- 179 | 4.04 | 0 | Hydrophobic |
| C7 | CD1 | TYR- 181 | 3.75 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 181 | 3.26 | 0 | Hydrophobic |
| C5 | CB | TYR- 181 | 3.74 | 0 | Hydrophobic |
| C6 | CB | TYR- 181 | 3.47 | 0 | Hydrophobic |
| C4 | CB | TYR- 188 | 3.56 | 0 | Hydrophobic |
| C13 | CB | LEU- 234 | 4.36 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 234 | 4.24 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 234 | 4.02 | 0 | Hydrophobic |
