sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2007-06-20
| 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: | 13.731 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.088 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.25 | 56.75 |
| According to VolSite | |
| HET Code: | 065 |
|---|---|
| Formula: | C28H36N2O9S |
| Molecular weight: | 576.658 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.08 % |
| Polar Surface area: | 141.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| 16.1192 | 22.7984 | 16.8002 |
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 | 4.14 | 0 | Hydrophobic |
| O18 | OD2 | ASP- 25 | 2.51 | 162.92 | H-Bond (Ligand Donor) |
| O18 | OD1 | ASP- 25 | 2.74 | 120.75 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.21 | 0 | Hydrophobic |
| C7 | CB | ALA- 28 | 3.45 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 4.31 | 0 | Hydrophobic |
| O39 | N | ASP- 30 | 3.24 | 129.68 | H-Bond (Protein Donor) |
| C40 | CB | ASP- 30 | 4.03 | 0 | Hydrophobic |
| C2 | CB | ASP- 30 | 4.12 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 32 | 3.67 | 0 | Hydrophobic |
| C40 | CG2 | ILE- 47 | 3.9 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 47 | 4.34 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 50 | 4.46 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 4.11 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.65 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 82 | 3.31 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 84 | 4.15 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 84 | 4.25 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 123 | 3.94 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 125 | 2.83 | 158.43 | H-Bond (Protein Donor) |
| N20 | O | GLY- 127 | 3.2 | 156.98 | H-Bond (Ligand Donor) |
| C25 | CB | ALA- 128 | 3.99 | 0 | Hydrophobic |
| C27 | CB | ASP- 129 | 4.13 | 0 | Hydrophobic |
| O28 | N | ASP- 129 | 3.02 | 162.8 | H-Bond (Protein Donor) |
| O26 | N | ASP- 130 | 3.35 | 158.33 | H-Bond (Protein Donor) |
| C25 | CG2 | VAL- 132 | 3.97 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 147 | 4.31 | 0 | Hydrophobic |
| C31 | CB | ILE- 147 | 4.44 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 150 | 3.98 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 182 | 3.43 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 184 | 4.41 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 184 | 4.21 | 0 | Hydrophobic |
