sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
1998-09-22
| 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 | 51 % |
| B | 49 % |
| B-Factor: | 24.444 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.009 | 752.625 |
| % Hydrophobic | % Polar |
|---|---|
| 46.19 | 53.81 |
| According to VolSite | |
| HET Code: | XV6 |
|---|---|
| Formula: | C41H38N6O5S2 |
| Molecular weight: | 758.908 g/mol |
| DrugBank ID: | DB02702 |
| Buried Surface Area: | 60.11 % |
| Polar Surface area: | 204.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 7 |
| Aromatic rings: | 6 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -9.26224 | 16.0105 | 27.9103 |
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 |
| O4 | OD1 | ASP- 25 | 2.8 | 157.94 | H-Bond (Ligand Donor) |
| O4 | OD2 | ASP- 25 | 3.32 | 130.79 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 25 | 3.12 | 158.03 | H-Bond (Ligand Donor) |
| O5 | OD2 | ASP- 25 | 2.94 | 141.68 | H-Bond (Ligand Donor) |
| C4 | CB | ALA- 28 | 4.39 | 0 | Hydrophobic |
| C5 | CB | ALA- 28 | 4.46 | 0 | Hydrophobic |
| C24 | CB | ALA- 28 | 3.4 | 0 | Hydrophobic |
| C74 | CB | ALA- 28 | 3.51 | 0 | Hydrophobic |
| S29 | CB | ASP- 29 | 4.14 | 0 | Hydrophobic |
| S79 | CB | ASP- 29 | 4.06 | 0 | Hydrophobic |
| O26 | N | ASP- 30 | 3.11 | 136.92 | H-Bond (Protein Donor) |
| O76 | N | ASP- 30 | 2.94 | 145.3 | H-Bond (Protein Donor) |
| C23 | CG2 | VAL- 32 | 3.83 | 0 | Hydrophobic |
| C74 | CG1 | VAL- 32 | 3.48 | 0 | Hydrophobic |
| S29 | CG2 | ILE- 47 | 4.16 | 0 | Hydrophobic |
| C72 | CG2 | ILE- 47 | 4.32 | 0 | Hydrophobic |
| S79 | CD1 | ILE- 47 | 3.5 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 47 | 4.18 | 0 | Hydrophobic |
| N26 | O | GLY- 48 | 3.07 | 162.76 | H-Bond (Ligand Donor) |
| N76 | O | GLY- 48 | 3.09 | 154 | H-Bond (Ligand Donor) |
| N27 | N | GLY- 48 | 3.12 | 169.27 | H-Bond (Protein Donor) |
| N77 | N | GLY- 48 | 3.16 | 154.1 | H-Bond (Protein Donor) |
| O1 | N | ILE- 50 | 3.11 | 151.65 | H-Bond (Protein Donor) |
| O1 | N | ILE- 50 | 3.03 | 172.44 | H-Bond (Protein Donor) |
| C33 | CG1 | ILE- 50 | 3.88 | 0 | Hydrophobic |
| C67 | CG1 | ILE- 50 | 3.55 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 50 | 3.54 | 0 | Hydrophobic |
| C75 | CD1 | ILE- 50 | 3.52 | 0 | Hydrophobic |
| C65 | CB | PRO- 81 | 4.11 | 0 | Hydrophobic |
| C66 | CG | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 4.05 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 84 | 4.34 | 0 | Hydrophobic |
| C61 | CG1 | VAL- 84 | 4.5 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 84 | 3.52 | 0 | Hydrophobic |
| C74 | CG1 | VAL- 84 | 3.52 | 0 | Hydrophobic |
