sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.250 Å
X-ray
2012-01-09
| 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 | 52 % |
| B | 48 % |
| B-Factor: | 13.213 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.911 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 40.93 | 59.07 |
| According to VolSite | |
| HET Code: | 031 |
|---|---|
| Formula: | C30H39N3O8S |
| Molecular weight: | 601.711 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.38 % |
| Polar Surface area: | 151.87 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -12.8497 | -20.2836 | 17.1086 |
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 |
| C33 | CD2 | LEU- 23 | 4.13 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 2.69 | 165.01 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.18 | 162.84 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.16 | 0 | Hydrophobic |
| C26 | CB | ALA- 28 | 4.24 | 0 | Hydrophobic |
| C6 | CB | ALA- 28 | 3.59 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 3.98 | 0 | Hydrophobic |
| C27 | CB | ASP- 29 | 4.3 | 0 | Hydrophobic |
| C29 | CB | ASP- 29 | 4.4 | 0 | Hydrophobic |
| O28 | N | ASP- 29 | 2.88 | 168.83 | H-Bond (Protein Donor) |
| O39 | N | ASP- 30 | 3.25 | 132.83 | H-Bond (Protein Donor) |
| C40 | CB | ASP- 30 | 3.9 | 0 | Hydrophobic |
| C2 | CB | ASP- 30 | 4.47 | 0 | Hydrophobic |
| C26 | CB | ASP- 30 | 4.42 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 32 | 4.38 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.8 | 0 | Hydrophobic |
| C40 | CG1 | VAL- 47 | 4.02 | 0 | Hydrophobic |
| C3 | CB | VAL- 47 | 4.33 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 47 | 3.55 | 0 | Hydrophobic |
| C47 | CG1 | ILE- 50 | 4.16 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 50 | 4.06 | 0 | Hydrophobic |
| C37 | CB | ILE- 50 | 4.35 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 4.05 | 0 | Hydrophobic |
| C47 | CG | PRO- 81 | 4.42 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.67 | 0 | Hydrophobic |
| C34 | CG1 | VAL- 82 | 3.55 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 4.44 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 84 | 3.98 | 0 | Hydrophobic |
| C47 | CG2 | ILE- 84 | 4.13 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 84 | 4.43 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.98 | 0 | Hydrophobic |
