sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.390 Å
X-ray
2011-01-27
| 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 | 50 % |
| B | 50 % |
| B-Factor: | 17.520 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.705 | 668.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.42 | 57.58 |
| According to VolSite | |
| HET Code: | NI7 |
|---|---|
| Formula: | C20H22N3O4 |
| Molecular weight: | 368.406 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.14 % |
| Polar Surface area: | 97.69 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -16.5998 | 20.2553 | -5.58667 |
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 |
| N27 | OD1 | ASP- 25 | 2.87 | 149.42 | H-Bond (Ligand Donor) |
| N27 | OD2 | ASP- 25 | 2.94 | 144.9 | H-Bond (Ligand Donor) |
| N27 | OD2 | ASP- 25 | 2.74 | 150.95 | H-Bond (Ligand Donor) |
| N27 | OD1 | ASP- 25 | 2.87 | 0 | Ionic (Ligand Cationic) |
| N27 | OD2 | ASP- 25 | 2.94 | 0 | Ionic (Ligand Cationic) |
| N27 | OD1 | ASP- 25 | 2.96 | 0 | Ionic (Ligand Cationic) |
| N27 | OD2 | ASP- 25 | 2.74 | 0 | Ionic (Ligand Cationic) |
| C8 | CB | ALA- 28 | 3.56 | 0 | Hydrophobic |
| C21 | CB | ALA- 28 | 3.43 | 0 | Hydrophobic |
| O9 | N | ASP- 30 | 3.06 | 152.05 | H-Bond (Protein Donor) |
| O22 | N | ASP- 30 | 3.12 | 153.11 | H-Bond (Protein Donor) |
| C10 | CG2 | VAL- 32 | 3.54 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 32 | 3.64 | 0 | Hydrophobic |
| C10 | CD1 | ILE- 47 | 4.46 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 47 | 4.33 | 0 | Hydrophobic |
| O14 | N | ILE- 50 | 2.99 | 157.64 | H-Bond (Protein Donor) |
| O16 | N | ILE- 50 | 3.42 | 142.71 | H-Bond (Protein Donor) |
| C11 | CD1 | ILE- 50 | 3.84 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 50 | 3.47 | 0 | Hydrophobic |
| C11 | CG2 | ILE- 84 | 4 | 0 | Hydrophobic |
| C24 | CG2 | ILE- 84 | 4 | 0 | Hydrophobic |
| O9 | O | HOH- 251 | 3.33 | 135.41 | H-Bond (Ligand Donor) |
