sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.140 Å
X-ray
2010-06-08
| 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 | 46 % |
| B | 54 % |
| B-Factor: | 12.747 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.005 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 40.53 | 59.47 |
| According to VolSite | |
| HET Code: | RIT |
|---|---|
| Formula: | C37H48N6O5S2 |
| Molecular weight: | 720.944 g/mol |
| DrugBank ID: | DB00503 |
| Buried Surface Area: | 61.66 % |
| Polar Surface area: | 202.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 20.1808 | 29.3845 | 12.7913 |
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 |
| S81 | CD | ARG- 8 | 4.26 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 8 | 3.5 | 18.34 | Pi/Cation |
| C35 | CD2 | LEU- 23 | 4.1 | 0 | Hydrophobic |
| C44 | CD2 | LEU- 23 | 4.24 | 0 | Hydrophobic |
| O41 | OD1 | ASP- 25 | 2.59 | 132.47 | H-Bond (Ligand Donor) |
| O41 | OD2 | ASP- 25 | 3.01 | 157.2 | H-Bond (Ligand Donor) |
| N58 | O | GLY- 27 | 3.14 | 145.29 | H-Bond (Ligand Donor) |
| C62 | CB | ALA- 28 | 3.72 | 0 | Hydrophobic |
| S3 | CB | ASP- 29 | 3.86 | 0 | Hydrophobic |
| O76 | N | ASP- 29 | 2.92 | 164 | H-Bond (Protein Donor) |
| C64 | CB | ASP- 30 | 4.18 | 0 | Hydrophobic |
| C64 | CG2 | VAL- 32 | 4.19 | 0 | Hydrophobic |
| C68 | CG2 | VAL- 32 | 4.34 | 0 | Hydrophobic |
| C64 | CD1 | ILE- 47 | 4.11 | 0 | Hydrophobic |
| N20 | O | GLY- 48 | 2.93 | 169.24 | H-Bond (Ligand Donor) |
| C31 | CB | ILE- 50 | 4.35 | 0 | Hydrophobic |
| C51 | CD1 | ILE- 50 | 3.99 | 0 | Hydrophobic |
| C52 | CG1 | ILE- 50 | 3.84 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 50 | 3.61 | 0 | Hydrophobic |
| C86 | CB | PRO- 81 | 4.05 | 0 | Hydrophobic |
| C90 | CB | PRO- 81 | 3.9 | 0 | Hydrophobic |
| C33 | CB | PRO- 81 | 4.07 | 0 | Hydrophobic |
| C50 | CG | PRO- 81 | 3.46 | 0 | Hydrophobic |
| S81 | CB | VAL- 82 | 4.06 | 0 | Hydrophobic |
| C90 | CB | VAL- 82 | 3.95 | 0 | Hydrophobic |
| C34 | CG1 | VAL- 82 | 3.27 | 0 | Hydrophobic |
| C52 | CG1 | VAL- 82 | 3.75 | 0 | Hydrophobic |
| C68 | CD1 | ILE- 84 | 3.92 | 0 | Hydrophobic |
| C52 | CD1 | ILE- 84 | 3.9 | 0 | Hydrophobic |
| C31 | CD1 | ILE- 84 | 3.76 | 0 | Hydrophobic |
