sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 Å
X-ray
2011-08-04
| 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: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 54.984 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.701 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 75.19 | 24.81 |
| According to VolSite | |
| HET Code: | M06 |
|---|---|
| Formula: | C20H14ClN5O2 |
| Molecular weight: | 391.810 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 76.97 % |
| Polar Surface area: | 94.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 8.55768 | 11.3826 | 17.2302 |
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 |
| CL | CB | PRO- 95 | 3.75 | 0 | Hydrophobic |
| CL | CD2 | LEU- 100 | 4.16 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 100 | 4.35 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 100 | 3.95 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 100 | 4.01 | 0 | Hydrophobic |
| N14 | N | ASN- 103 | 2.9 | 165.69 | H-Bond (Protein Donor) |
| N15 | O | ASN- 103 | 2.74 | 162.69 | H-Bond (Ligand Donor) |
| C6 | CB | VAL- 106 | 4.48 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 106 | 3.94 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 108 | 3.84 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 179 | 4.09 | 0 | Hydrophobic |
| C6 | CD2 | TYR- 181 | 3.78 | 0 | Hydrophobic |
| CL | CD1 | TYR- 188 | 4.04 | 0 | Hydrophobic |
| C6 | CB | TYR- 188 | 3.87 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 3.43 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 188 | 3.81 | 0 | Aromatic Face/Face |
| C20 | CB | PRO- 225 | 4.01 | 0 | Hydrophobic |
| CL | CH2 | TRP- 229 | 3.72 | 0 | Hydrophobic |
| C9 | CB | TRP- 229 | 4.21 | 0 | Hydrophobic |
| C21 | CB | LEU- 234 | 4.24 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 234 | 3.43 | 0 | Hydrophobic |
| C22 | CZ | TYR- 318 | 3.26 | 0 | Hydrophobic |
