sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2007-07-19
| 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 | 53 % |
| B | 47 % |
| B-Factor: | 20.487 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.924 | 826.875 |
| % Hydrophobic | % Polar |
|---|---|
| 42.86 | 57.14 |
| According to VolSite | |
| HET Code: | QN3 |
|---|---|
| Formula: | C30H30Cl2N3O4S2 |
| Molecular weight: | 631.613 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.44 % |
| Polar Surface area: | 108.13 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -17.4085 | 19.6164 | -5.78166 |
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 |
| C30 | CD2 | LEU- 23 | 3.93 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 23 | 3.82 | 0 | Hydrophobic |
| N22 | OD1 | ASP- 25 | 2.96 | 0 | Ionic (Ligand Cationic) |
| N22 | OD2 | ASP- 25 | 2.51 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 25 | 2.82 | 0 | Ionic (Ligand Cationic) |
| N22 | OD2 | ASP- 25 | 2.89 | 0 | Ionic (Ligand Cationic) |
| N22 | OD2 | ASP- 25 | 2.51 | 145.71 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 25 | 2.82 | 145.63 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 25 | 2.89 | 122.58 | H-Bond (Ligand Donor) |
| C7 | CB | ALA- 28 | 4.34 | 0 | Hydrophobic |
| C6 | CB | ALA- 28 | 3.53 | 0 | Hydrophobic |
| CL1 | CB | ALA- 28 | 3.35 | 0 | Hydrophobic |
| C4 | CB | ASP- 29 | 4.43 | 0 | Hydrophobic |
| C1 | CB | ASP- 30 | 4.2 | 0 | Hydrophobic |
| C2 | CG2 | VAL- 32 | 3.9 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 32 | 3.42 | 0 | Hydrophobic |
| C3 | CB | ILE- 47 | 4.33 | 0 | Hydrophobic |
| C4 | CG2 | ILE- 47 | 4.33 | 0 | Hydrophobic |
| C13 | CB | ILE- 50 | 4.04 | 0 | Hydrophobic |
| C27 | CG1 | ILE- 50 | 3.79 | 0 | Hydrophobic |
| O40 | N | ILE- 50 | 3.05 | 162.72 | H-Bond (Protein Donor) |
| C29 | CG | PRO- 81 | 4.12 | 0 | Hydrophobic |
| C35 | CG | PRO- 81 | 3.44 | 0 | Hydrophobic |
| C35 | CG | PRO- 81 | 3.44 | 0 | Hydrophobic |
| C38 | CG1 | VAL- 82 | 3.99 | 0 | Hydrophobic |
| C30 | CG1 | VAL- 82 | 3.66 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 84 | 3.89 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 84 | 3.99 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 84 | 3.45 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 84 | 3.24 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 84 | 3.52 | 0 | Hydrophobic |
