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
2001-10-17
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1Y2 |
| AC: | P35963 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 362651 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 23.089 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.345 | 1194.750 |
| % Hydrophobic | % Polar |
|---|---|
| 43.50 | 56.50 |
| According to VolSite | |
| HET Code: | XN2 |
|---|---|
| Formula: | C39H51N4O6 |
| Molecular weight: | 671.845 g/mol |
| DrugBank ID: | DB01721 |
| Buried Surface Area: | 63.97 % |
| Polar Surface area: | 124.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 4.88867 | -2.1661 | 13.9861 |
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 |
| C16 | CD2 | LEU- 23 | 3.78 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 23 | 4.47 | 0 | Hydrophobic |
| N3 | OD2 | ASP- 25 | 3.88 | 0 | Ionic (Ligand Cationic) |
| O2 | OD2 | ASP- 25 | 3.02 | 143.41 | H-Bond (Ligand Donor) |
| O2 | OD1 | ASP- 25 | 2.56 | 135.09 | H-Bond (Ligand Donor) |
| N4 | O | GLY- 27 | 3.37 | 151.18 | H-Bond (Ligand Donor) |
| C5 | CB | ALA- 28 | 4.03 | 0 | Hydrophobic |
| C6 | CB | ALA- 28 | 3.93 | 0 | Hydrophobic |
| C29 | CB | ALA- 28 | 3.54 | 0 | Hydrophobic |
| O4 | N | ASP- 29 | 3.13 | 154.01 | H-Bond (Protein Donor) |
| O4 | OD2 | ASP- 29 | 3.02 | 167.69 | H-Bond (Ligand Donor) |
| C24 | CB | ASP- 29 | 4.35 | 0 | Hydrophobic |
| C5 | CB | ASP- 30 | 4.29 | 0 | Hydrophobic |
| C26 | CB | ASP- 30 | 3.67 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 32 | 4.09 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 3.93 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 4.45 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 47 | 3.91 | 0 | Hydrophobic |
| C38 | CA | GLY- 48 | 4.15 | 0 | Hydrophobic |
| C35 | CA | GLY- 48 | 3.98 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 50 | 3.56 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 50 | 3.91 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 50 | 4.05 | 0 | Hydrophobic |
| C38 | CZ | PHE- 53 | 3.39 | 0 | Hydrophobic |
| C19 | CG | PRO- 81 | 3.74 | 0 | Hydrophobic |
| C32 | CB | PRO- 81 | 3.47 | 0 | Hydrophobic |
| C33 | CG2 | THR- 82 | 4.19 | 0 | Hydrophobic |
| C39 | CG2 | THR- 82 | 4.05 | 0 | Hydrophobic |
| C15 | CG2 | THR- 82 | 4.15 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 84 | 4.45 | 0 | Hydrophobic |
| C39 | CG2 | VAL- 84 | 3.45 | 0 | Hydrophobic |
| N2 | O | HOH- 530 | 3.06 | 160.88 | H-Bond (Ligand Donor) |
