sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2011-02-11
| 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: | 14.975 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.131 | 786.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.07 | 51.93 |
| According to VolSite | |
| HET Code: | NI8 |
|---|---|
| Formula: | C22H26N3O4 |
| Molecular weight: | 396.460 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.38 % |
| Polar Surface area: | 97.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -16.9801 | 20.0784 | -5.98245 |
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 |
| N27 | OD1 | ASP- 25 | 3.17 | 153.37 | H-Bond (Ligand Donor) |
| N27 | OD2 | ASP- 25 | 3.17 | 147.39 | H-Bond (Ligand Donor) |
| N27 | OD2 | ASP- 25 | 2.77 | 163.94 | H-Bond (Ligand Donor) |
| N27 | OD1 | ASP- 25 | 3.17 | 0 | Ionic (Ligand Cationic) |
| N27 | OD2 | ASP- 25 | 3.17 | 0 | Ionic (Ligand Cationic) |
| N27 | OD1 | ASP- 25 | 3.14 | 0 | Ionic (Ligand Cationic) |
| N27 | OD2 | ASP- 25 | 2.77 | 0 | Ionic (Ligand Cationic) |
| C23 | CB | ALA- 28 | 3.81 | 0 | Hydrophobic |
| C23 | CB | ALA- 28 | 3.81 | 0 | Hydrophobic |
| C11 | CB | ALA- 28 | 3.83 | 0 | Hydrophobic |
| C22 | CB | ASP- 29 | 4.08 | 0 | Hydrophobic |
| O29 | N | ASP- 29 | 2.92 | 172 | H-Bond (Protein Donor) |
| C9 | CB | ASP- 30 | 3.7 | 0 | Hydrophobic |
| O30 | N | ASP- 30 | 2.95 | 136.05 | H-Bond (Protein Donor) |
| O30 | OD2 | ASP- 30 | 2.71 | 156.79 | H-Bond (Ligand Donor) |
| C8 | CG2 | VAL- 32 | 4.29 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 32 | 3.32 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 32 | 4.31 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 47 | 3.89 | 0 | Hydrophobic |
| C22 | CB | ILE- 47 | 4.4 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 47 | 4.36 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 47 | 4.02 | 0 | Hydrophobic |
| O16 | N | ILE- 50 | 3.11 | 151.67 | H-Bond (Protein Donor) |
| C12 | CG1 | ILE- 50 | 3.71 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 50 | 3.97 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 84 | 4.01 | 0 | Hydrophobic |
| O14 | O | HOH- 231 | 3.05 | 179.97 | H-Bond (Protein Donor) |
