sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.320 Å
X-ray
2011-08-29
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 16.279 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.039 | 901.125 |
| % Hydrophobic | % Polar |
|---|---|
| 44.19 | 55.81 |
| According to VolSite | |
| HET Code: | ROC |
|---|---|
| Formula: | C38H51N6O5 |
| Molecular weight: | 671.849 g/mol |
| DrugBank ID: | DB01232 |
| Buried Surface Area: | 68.64 % |
| Polar Surface area: | 167.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -10.528 | 19.7908 | -18.0503 |
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 |
| C7A | CD2 | LEU- 23 | 4.21 | 0 | Hydrophobic |
| CD2 | CD2 | LEU- 23 | 3.76 | 0 | Hydrophobic |
| O2 | OD1 | ASP- 25 | 2.58 | 154.69 | H-Bond (Protein Donor) |
| O2 | OD1 | ASP- 25 | 2.83 | 123.52 | H-Bond (Ligand Donor) |
| O2 | OD2 | ASP- 25 | 2.72 | 157.89 | H-Bond (Ligand Donor) |
| N2 | O | GLY- 27 | 3.42 | 166.35 | H-Bond (Ligand Donor) |
| C11 | CB | ALA- 28 | 4.17 | 0 | Hydrophobic |
| C22 | CB | ALA- 28 | 4.01 | 0 | Hydrophobic |
| O | N | ASP- 29 | 2.94 | 162.44 | H-Bond (Protein Donor) |
| OD1 | N | ASP- 30 | 3.06 | 157.1 | H-Bond (Protein Donor) |
| ND2 | OD2 | ASP- 30 | 3.25 | 159.11 | H-Bond (Ligand Donor) |
| C11 | CB | ASP- 30 | 4.07 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 32 | 3.92 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 32 | 4.08 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 47 | 4.16 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 47 | 3.72 | 0 | Hydrophobic |
| N | O | GLY- 48 | 3.08 | 131.16 | H-Bond (Ligand Donor) |
| C71 | CG1 | ILE- 50 | 4 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 50 | 3.29 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 50 | 3.29 | 0 | Hydrophobic |
| CD1 | CG1 | ILE- 50 | 3.76 | 0 | Hydrophobic |
| C61 | CD1 | ILE- 50 | 3.3 | 0 | Hydrophobic |
| CE1 | CG | PRO- 81 | 4.44 | 0 | Hydrophobic |
| CZ | CB | PRO- 81 | 4.45 | 0 | Hydrophobic |
| C7 | CB | PRO- 81 | 3.73 | 0 | Hydrophobic |
| C51 | CG | PRO- 81 | 3.68 | 0 | Hydrophobic |
| C41 | CG2 | VAL- 82 | 3.9 | 0 | Hydrophobic |
| C61 | CB | VAL- 82 | 4.25 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 82 | 4.02 | 0 | Hydrophobic |
| CE2 | CB | VAL- 82 | 3.79 | 0 | Hydrophobic |
| CB | CD1 | ILE- 84 | 4.42 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 84 | 3.82 | 0 | Hydrophobic |
| C71 | CG2 | ILE- 84 | 3.64 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 84 | 3.52 | 0 | Hydrophobic |
