sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-11-17
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1Z2 |
| AC: | P12499 |
| Organism: | Human immunodeficiency virus type 1 group M subtype D |
| Reign: | Viruses |
| TaxID: | 11683 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 48 % |
| B | 52 % |
| B-Factor: | 11.226 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.204 | 1063.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.27 | 58.73 |
| According to VolSite | |
| HET Code: | G40 |
|---|---|
| Formula: | C38H53N5O6S |
| Molecular weight: | 707.922 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.68 % |
| Polar Surface area: | 177.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 13.3708 | 21.9711 | 6.36042 |
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 |
| C27 | CD2 | LEU- 23 | 4.18 | 0 | Hydrophobic |
| C8 | CB | ALA- 28 | 3.47 | 0 | Hydrophobic |
| O12 | N | ASP- 29 | 2.81 | 172.83 | H-Bond (Protein Donor) |
| C8 | CB | ASP- 30 | 4.43 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 32 | 4.48 | 0 | Hydrophobic |
| C7 | CB | ILE- 47 | 3.49 | 0 | Hydrophobic |
| N10 | O | GLY- 48 | 2.88 | 171.7 | H-Bond (Ligand Donor) |
| C47 | CG1 | ILE- 50 | 3.42 | 0 | Hydrophobic |
| S54 | CB | PRO- 81 | 4.37 | 0 | Hydrophobic |
| C30 | CG | PRO- 81 | 3.25 | 0 | Hydrophobic |
| C28 | CG2 | THR- 82 | 3.5 | 0 | Hydrophobic |
| C33 | CG2 | THR- 82 | 3.57 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 84 | 4.33 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 123 | 3.31 | 0 | Hydrophobic |
| O22 | OD2 | ASP- 125 | 2.78 | 161.04 | H-Bond (Ligand Donor) |
| N43 | O | GLY- 127 | 3.17 | 148.72 | H-Bond (Ligand Donor) |
| C46 | CB | ALA- 128 | 4 | 0 | Hydrophobic |
| C36 | CB | ASP- 129 | 4.27 | 0 | Hydrophobic |
| O39 | N | ASP- 129 | 2.87 | 169.25 | H-Bond (Protein Donor) |
| C45 | CB | ASP- 130 | 4.44 | 0 | Hydrophobic |
| C46 | CG1 | VAL- 132 | 4.35 | 0 | Hydrophobic |
| C45 | CD1 | ILE- 147 | 4.44 | 0 | Hydrophobic |
| C47 | CD1 | ILE- 147 | 3.94 | 0 | Hydrophobic |
| N40 | O | GLY- 148 | 3.01 | 177.12 | H-Bond (Ligand Donor) |
| C13 | CG1 | ILE- 150 | 3.38 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 150 | 4.23 | 0 | Hydrophobic |
| S54 | CZ | PHE- 153 | 3.22 | 0 | Hydrophobic |
| C18 | CG | PRO- 181 | 3.53 | 0 | Hydrophobic |
| C19 | CG2 | THR- 182 | 3.59 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 184 | 4.37 | 0 | Hydrophobic |
| C46 | CG2 | VAL- 184 | 4.01 | 0 | Hydrophobic |
