sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-01-14
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1A2 |
| AC: | P03369 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11685 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 60 % |
| B | 40 % |
| B-Factor: | 14.112 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.799 | 793.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.85 | 59.15 |
| According to VolSite | |
| HET Code: | DRS |
|---|---|
| Formula: | C19H25N2O5 |
| Molecular weight: | 361.412 g/mol |
| DrugBank ID: | DB07679 |
| Buried Surface Area: | 60.04 % |
| Polar Surface area: | 107.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 5.20896 | 1.91831 | 11.8025 |
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 |
| N | O | GLY- 27 | 2.83 | 157.35 | H-Bond (Ligand Donor) |
| CAB | CB | ALA- 28 | 3.64 | 0 | Hydrophobic |
| OAC | N | ASP- 29 | 2.9 | 162.19 | H-Bond (Protein Donor) |
| CAA | CB | ASP- 30 | 4.3 | 0 | Hydrophobic |
| CAA | CG2 | VAL- 32 | 4.12 | 0 | Hydrophobic |
| CAB | CG2 | VAL- 32 | 4.37 | 0 | Hydrophobic |
| CAA | CD1 | ILE- 47 | 4.14 | 0 | Hydrophobic |
| NAP | O | GLY- 48 | 2.87 | 152.32 | H-Bond (Ligand Donor) |
| CAB | CG2 | ILE- 84 | 4.44 | 0 | Hydrophobic |
| CD2 | CD2 | LEU- 123 | 3.51 | 0 | Hydrophobic |
| CAB | CG1 | ILE- 150 | 4.04 | 0 | Hydrophobic |
| CAM | CG | PRO- 181 | 3.88 | 0 | Hydrophobic |
| CE1 | CG | PRO- 181 | 3.6 | 0 | Hydrophobic |
| CZ | CG2 | VAL- 182 | 3.97 | 0 | Hydrophobic |
| CB | CD1 | ILE- 184 | 3.72 | 0 | Hydrophobic |
