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
1996-09-16
| 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: | 19.663 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.471 | 398.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.22 | 56.78 |
| According to VolSite | |
| HET Code: | 0E8 |
|---|---|
| Formula: | C30H46N3O6 |
| Molecular weight: | 544.703 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.73 % |
| Polar Surface area: | 133.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 16 |
| X | Y | Z |
|---|---|---|
| -9.44174 | 16.4365 | 27.8202 |
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 |
| CB | CD1 | LEU- 23 | 3.83 | 0 | Hydrophobic |
| CB1 | CD1 | LEU- 23 | 3.83 | 0 | Hydrophobic |
| CD21 | CD1 | LEU- 23 | 4.37 | 0 | Hydrophobic |
| O | OD2 | ASP- 25 | 2.65 | 152.27 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 25 | 2.92 | 153.72 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 25 | 2.78 | 139.27 | H-Bond (Ligand Donor) |
| N1 | OD1 | ASP- 25 | 2.7 | 142.33 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 25 | 3.17 | 153.51 | H-Bond (Ligand Donor) |
| O3 | OD2 | ASP- 25 | 2.56 | 161.09 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 25 | 2.92 | 0 | Ionic (Ligand Cationic) |
| N1 | OD1 | ASP- 25 | 2.78 | 0 | Ionic (Ligand Cationic) |
| N1 | OD1 | ASP- 25 | 2.7 | 0 | Ionic (Ligand Cationic) |
| N1 | OD2 | ASP- 25 | 3.17 | 0 | Ionic (Ligand Cationic) |
| N | O | GLY- 27 | 3.12 | 128.93 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 27 | 3.28 | 132.15 | H-Bond (Ligand Donor) |
| C3 | CB | ALA- 28 | 4.49 | 0 | Hydrophobic |
| C11 | CB | ALA- 28 | 4.32 | 0 | Hydrophobic |
| C32 | CB | ALA- 28 | 4.48 | 0 | Hydrophobic |
| C2 | CB | ASP- 30 | 3.9 | 0 | Hydrophobic |
| C32 | CB | ASP- 30 | 3.99 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 32 | 3.96 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 32 | 3.79 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 32 | 4.35 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 47 | 4.13 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 47 | 3.75 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 50 | 4.36 | 0 | Hydrophobic |
| C22 | CG1 | ILE- 50 | 3.97 | 0 | Hydrophobic |
| CD1 | CG2 | ILE- 50 | 4.03 | 0 | Hydrophobic |
| CD11 | CD1 | ILE- 50 | 3.69 | 0 | Hydrophobic |
| CZ | CB | PRO- 81 | 3.94 | 0 | Hydrophobic |
| CE1 | CG | PRO- 81 | 3.38 | 0 | Hydrophobic |
| CE11 | CG | PRO- 81 | 3.26 | 0 | Hydrophobic |
| CZ1 | CB | PRO- 81 | 3.47 | 0 | Hydrophobic |
| CG | CB | ALA- 82 | 4.45 | 0 | Hydrophobic |
| CD21 | CB | ALA- 82 | 3.82 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 84 | 4.45 | 0 | Hydrophobic |
| CB | CD1 | ILE- 84 | 4.48 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 84 | 4.35 | 0 | Hydrophobic |
| O11 | O | HOH- 301 | 3.15 | 179.97 | H-Bond (Protein Donor) |
