sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1996-11-01
| 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 | 49 % |
| B | 51 % |
| B-Factor: | 16.110 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.726 | 631.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.18 | 58.82 |
| According to VolSite | |
| HET Code: | DMQ |
|---|---|
| Formula: | C33H36N4O3 |
| Molecular weight: | 536.664 g/mol |
| DrugBank ID: | DB02102 |
| Buried Surface Area: | 74.52 % |
| Polar Surface area: | 116.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -9.38723 | 16.3091 | 27.8436 |
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 | CD1 | LEU- 23 | 4.26 | 0 | Hydrophobic |
| O4 | OD2 | ASP- 25 | 2.81 | 162.81 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 25 | 2.97 | 171.79 | H-Bond (Ligand Donor) |
| O5 | OD2 | ASP- 25 | 3.41 | 131.02 | H-Bond (Ligand Donor) |
| C23 | CB | ALA- 28 | 3.35 | 0 | Hydrophobic |
| C78 | CB | ALA- 28 | 3.7 | 0 | Hydrophobic |
| C23 | CB | ASP- 30 | 4.44 | 0 | Hydrophobic |
| C77 | CB | ASP- 30 | 3.97 | 0 | Hydrophobic |
| N29 | OD1 | ASP- 30 | 2.78 | 130.98 | H-Bond (Ligand Donor) |
| N79 | OD2 | ASP- 30 | 3.01 | 155.16 | H-Bond (Ligand Donor) |
| C23 | CG2 | VAL- 32 | 3.86 | 0 | Hydrophobic |
| C78 | CG2 | VAL- 32 | 3.53 | 0 | Hydrophobic |
| C28 | CD1 | ILE- 47 | 3.65 | 0 | Hydrophobic |
| C77 | CD1 | ILE- 47 | 3.75 | 0 | Hydrophobic |
| O1 | N | ILE- 50 | 2.89 | 132.79 | H-Bond (Protein Donor) |
| C79 | CG1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C21 | CD1 | ILE- 50 | 3.57 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 50 | 3.37 | 0 | Hydrophobic |
| C34 | CG | PRO- 81 | 3.47 | 0 | Hydrophobic |
| C66 | CG | PRO- 81 | 3.89 | 0 | Hydrophobic |
| C65 | CG2 | VAL- 82 | 4.2 | 0 | Hydrophobic |
| C35 | CG1 | VAL- 82 | 3.61 | 0 | Hydrophobic |
| C78 | CG2 | ILE- 84 | 3.98 | 0 | Hydrophobic |
| C79 | CD1 | ILE- 84 | 4.15 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.67 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 84 | 3.79 | 0 | Hydrophobic |
| C61 | CD1 | ILE- 84 | 4.06 | 0 | Hydrophobic |
