sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2007-06-16
| 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 | 48 % |
| B | 52 % |
| B-Factor: | 21.372 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.788 | 749.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.99 | 59.01 |
| According to VolSite | |
| HET Code: | 1UN |
|---|---|
| Formula: | C32H46N3O4S |
| Molecular weight: | 568.790 g/mol |
| DrugBank ID: | DB00220 |
| Buried Surface Area: | 73.98 % |
| Polar Surface area: | 128.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| -13.1522 | 53.7642 | 3.55253 |
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 |
| C82 | CD2 | LEU- 23 | 3.86 | 0 | Hydrophobic |
| O21 | OD2 | ASP- 25 | 2.66 | 159.17 | H-Bond (Protein Donor) |
| O21 | OD1 | ASP- 25 | 2.78 | 151.36 | H-Bond (Ligand Donor) |
| O21 | OD2 | ASP- 25 | 2.71 | 130.64 | H-Bond (Ligand Donor) |
| N22 | O | GLY- 27 | 3.34 | 158.35 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 28 | 3.87 | 0 | Hydrophobic |
| C16 | CB | ALA- 28 | 4.02 | 0 | Hydrophobic |
| C39 | CB | ALA- 28 | 3.7 | 0 | Hydrophobic |
| C34 | CB | ALA- 28 | 3.81 | 0 | Hydrophobic |
| C32 | CB | ASP- 29 | 3.91 | 0 | Hydrophobic |
| C16 | CB | ASN- 30 | 3.87 | 0 | Hydrophobic |
| C33 | CB | ASN- 30 | 4.38 | 0 | Hydrophobic |
| O38 | ND2 | ASN- 30 | 3.02 | 147.31 | H-Bond (Protein Donor) |
| O38 | N | ASN- 30 | 3.39 | 135.27 | H-Bond (Protein Donor) |
| C14 | CG2 | VAL- 32 | 3.84 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 32 | 4.5 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 32 | 3.84 | 0 | Hydrophobic |
| C39 | CG2 | VAL- 32 | 4.28 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 47 | 3.74 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 47 | 4.42 | 0 | Hydrophobic |
| C4 | CB | ILE- 50 | 4.44 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 50 | 3.57 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 50 | 3.76 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 50 | 4.08 | 0 | Hydrophobic |
| S74 | CG1 | ILE- 50 | 4.13 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 50 | 3.61 | 0 | Hydrophobic |
| C3 | CG | PRO- 81 | 3.85 | 0 | Hydrophobic |
| C5 | CG | PRO- 81 | 3.92 | 0 | Hydrophobic |
| C79 | CG | PRO- 81 | 4.06 | 0 | Hydrophobic |
| C80 | CG1 | VAL- 82 | 3.75 | 0 | Hydrophobic |
| C81 | CG2 | VAL- 82 | 3.9 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 82 | 3.43 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 84 | 4.1 | 0 | Hydrophobic |
| C39 | CD1 | ILE- 84 | 4.27 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 84 | 3.44 | 0 | Hydrophobic |
| S74 | CD1 | ILE- 84 | 3.84 | 0 | Hydrophobic |
| C82 | CD1 | ILE- 84 | 3.86 | 0 | Hydrophobic |
