sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
1994-10-19
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV2RO |
| AC: | P04584 |
| Organism: | Human immunodeficiency virus type 2 subtype A |
| Reign: | Viruses |
| TaxID: | 11720 |
| EC Number: | 3.4.23.47 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 12.019 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 789.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.02 | 55.98 |
| According to VolSite | |
| HET Code: | 0PO |
|---|---|
| Formula: | C41H53N6O4S |
| Molecular weight: | 725.962 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.47 % |
| Polar Surface area: | 163.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 50.8012 | 22.702 | 4.22402 |
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 |
| CD1 | CD2 | LEU- 23 | 3.99 | 0 | Hydrophobic |
| OXT | OD2 | ASP- 25 | 2.66 | 155.41 | H-Bond (Ligand Donor) |
| OXT | OD1 | ASP- 25 | 2.98 | 123.62 | H-Bond (Ligand Donor) |
| OXT | OD1 | ASP- 25 | 2.58 | 163.35 | H-Bond (Protein Donor) |
| N2 | O | GLY- 27 | 3.2 | 160.63 | H-Bond (Ligand Donor) |
| C2' | CB | ALA- 28 | 4.18 | 0 | Hydrophobic |
| C3' | CB | ALA- 28 | 4.12 | 0 | Hydrophobic |
| CG1 | CB | ALA- 28 | 4.02 | 0 | Hydrophobic |
| O1 | N | ASP- 29 | 2.81 | 156.82 | H-Bond (Protein Donor) |
| CG2 | CB | ASP- 30 | 4.13 | 0 | Hydrophobic |
| C2' | CB | ASP- 30 | 3.85 | 0 | Hydrophobic |
| CG1 | CG2 | ILE- 32 | 4.31 | 0 | Hydrophobic |
| C3' | CG2 | ILE- 32 | 4.05 | 0 | Hydrophobic |
| CG2 | CG2 | VAL- 47 | 3.95 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 47 | 4.28 | 0 | Hydrophobic |
| C4' | CG2 | VAL- 47 | 3.73 | 0 | Hydrophobic |
| N | O | GLY- 48 | 3.18 | 141.13 | H-Bond (Ligand Donor) |
| CD2 | CD1 | ILE- 50 | 4.5 | 0 | Hydrophobic |
| CE2 | CG1 | ILE- 50 | 4.42 | 0 | Hydrophobic |
| C3' | CD1 | ILE- 50 | 3.48 | 0 | Hydrophobic |
| C4' | CD1 | ILE- 50 | 3.52 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 50 | 3.71 | 0 | Hydrophobic |
| C52 | CB | PRO- 81 | 3.65 | 0 | Hydrophobic |
| S | CG | PRO- 81 | 3.57 | 0 | Hydrophobic |
| C6 | CB | PRO- 81 | 3.68 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.68 | 0 | Hydrophobic |
| CZ | CG | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C42 | CG | PRO- 81 | 3.67 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 82 | 3.99 | 0 | Hydrophobic |
| CE1 | CG1 | ILE- 82 | 3.95 | 0 | Hydrophobic |
| C41 | CG2 | ILE- 82 | 3.68 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 84 | 3.65 | 0 | Hydrophobic |
| CG | CG2 | ILE- 84 | 4.45 | 0 | Hydrophobic |
| C51 | CD1 | ILE- 84 | 3.71 | 0 | Hydrophobic |
| C3' | CG1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
