sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2002-09-19
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1BR |
| AC: | P03367 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11686 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 20.360 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.120 | 766.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.58 | 52.42 |
| According to VolSite | |
| HET Code: | JE2 |
|---|---|
| Formula: | C32H37N3O5S |
| Molecular weight: | 575.718 g/mol |
| DrugBank ID: | DB02668 |
| Buried Surface Area: | 73.58 % |
| Polar Surface area: | 144.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 16.3358 | 22.8855 | 17.2749 |
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 |
| C19 | CD2 | LEU- 23 | 4 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 23 | 3.43 | 0 | Hydrophobic |
| O23 | OD2 | ASP- 25 | 2.59 | 153.36 | H-Bond (Protein Donor) |
| O21 | OD1 | ASP- 25 | 2.57 | 156.63 | H-Bond (Ligand Donor) |
| O21 | OD2 | ASP- 25 | 3.18 | 128.93 | H-Bond (Ligand Donor) |
| N11 | O | GLY- 27 | 2.98 | 158.94 | H-Bond (Ligand Donor) |
| C8 | CB | ALA- 28 | 3.56 | 0 | Hydrophobic |
| C20 | CB | ALA- 28 | 4.48 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.73 | 0 | Hydrophobic |
| C37 | CB | ALA- 28 | 3.76 | 0 | Hydrophobic |
| C3 | CB | ASP- 29 | 3.78 | 0 | Hydrophobic |
| C1 | CB | ASP- 30 | 4.44 | 0 | Hydrophobic |
| C38 | CB | ASP- 30 | 3.62 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 30 | 2.66 | 164.77 | H-Bond (Ligand Donor) |
| O2 | N | ASP- 30 | 3.4 | 136.61 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 32 | 3.84 | 0 | Hydrophobic |
| C37 | CG1 | VAL- 32 | 3.79 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 47 | 4.32 | 0 | Hydrophobic |
| C39 | CG2 | ILE- 47 | 3.76 | 0 | Hydrophobic |
| C40 | CB | ILE- 47 | 3.6 | 0 | Hydrophobic |
| C1 | CB | ILE- 47 | 4.13 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 47 | 4.16 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 50 | 4.02 | 0 | Hydrophobic |
| S26 | CG1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C41 | CD1 | ILE- 50 | 4.02 | 0 | Hydrophobic |
| C15 | CB | ILE- 50 | 4.22 | 0 | Hydrophobic |
| C38 | CD1 | LEU- 76 | 3.96 | 0 | Hydrophobic |
| C17 | CB | PRO- 81 | 3.88 | 0 | Hydrophobic |
| C16 | CG | PRO- 81 | 4.17 | 0 | Hydrophobic |
| C29 | CB | PRO- 81 | 4.1 | 0 | Hydrophobic |
| S26 | CG | PRO- 81 | 3.96 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 82 | 4.09 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 82 | 3.6 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 84 | 4.2 | 0 | Hydrophobic |
| S26 | CD1 | ILE- 84 | 3.67 | 0 | Hydrophobic |
| C41 | CD1 | ILE- 84 | 3.85 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.68 | 0 | Hydrophobic |
| N33 | O | HOH- 1003 | 2.88 | 169.82 | H-Bond (Ligand Donor) |
