sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1997-04-25
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1H2 |
| AC: | P04585 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11706 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| B | 45 % |
| B-Factor: | 26.569 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.033 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.90 | 53.10 |
| According to VolSite | |
| HET Code: | 846 |
|---|---|
| Formula: | C34H36N4O4S |
| Molecular weight: | 596.739 g/mol |
| DrugBank ID: | DB04609 |
| Buried Surface Area: | 60.92 % |
| Polar Surface area: | 134.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -9.59816 | 15.1497 | 29.9201 |
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 |
| C37 | CD2 | LEU- 23 | 4.14 | 0 | Hydrophobic |
| C63 | CD2 | LEU- 23 | 4.13 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 25 | 2.97 | 130.34 | H-Bond (Ligand Donor) |
| O4 | OD1 | ASP- 25 | 2.94 | 153.53 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 25 | 2.82 | 156.76 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 25 | 3.16 | 123.65 | H-Bond (Ligand Donor) |
| C4 | CB | ALA- 28 | 4.43 | 0 | Hydrophobic |
| C5 | CB | ALA- 28 | 4.46 | 0 | Hydrophobic |
| C24 | CB | ALA- 28 | 3.54 | 0 | Hydrophobic |
| C70 | CB | ALA- 28 | 3.98 | 0 | Hydrophobic |
| O26 | N | ASP- 29 | 3.46 | 137.99 | H-Bond (Protein Donor) |
| S29 | CB | ASP- 29 | 4.49 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.32 | 150.61 | H-Bond (Protein Donor) |
| C72 | CG1 | VAL- 32 | 4.27 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 32 | 3.71 | 0 | Hydrophobic |
| C71 | CD1 | ILE- 47 | 4.35 | 0 | Hydrophobic |
| S29 | CG2 | ILE- 47 | 4.3 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 47 | 4.14 | 0 | Hydrophobic |
| N26 | O | GLY- 48 | 3.2 | 170.96 | H-Bond (Ligand Donor) |
| N27 | N | GLY- 48 | 3.13 | 165.52 | H-Bond (Protein Donor) |
| C67 | CD1 | ILE- 50 | 3.97 | 0 | Hydrophobic |
| C72 | CD1 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 50 | 3.44 | 0 | Hydrophobic |
| O1 | N | ILE- 50 | 3.19 | 144.87 | H-Bond (Protein Donor) |
| C66 | CG | PRO- 81 | 4.4 | 0 | Hydrophobic |
| C35 | CG2 | VAL- 82 | 3.55 | 0 | Hydrophobic |
| C65 | CG1 | VAL- 82 | 3.51 | 0 | Hydrophobic |
| C72 | CD1 | ILE- 84 | 4.01 | 0 | Hydrophobic |
| C24 | CG1 | ILE- 84 | 4.19 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 84 | 3.71 | 0 | Hydrophobic |
| C61 | CD1 | ILE- 84 | 3.76 | 0 | Hydrophobic |
