sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2015-02-23
| 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 | 50 % |
| B | 50 % |
| B-Factor: | 15.087 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.043 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.08 | 57.92 |
| According to VolSite | |
| HET Code: | G04 |
|---|---|
| Formula: | C29H40N2O9S |
| Molecular weight: | 592.701 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.11 % |
| Polar Surface area: | 141.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| -7.61663 | -15.7326 | -1.05983 |
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 |
| C15 | CD2 | LEU- 23 | 3.76 | 0 | Hydrophobic |
| C33 | CD2 | LEU- 23 | 3.69 | 0 | Hydrophobic |
| O18 | OD1 | ASP- 25 | 3 | 157.5 | H-Bond (Protein Donor) |
| N20 | O | GLY- 27 | 3.07 | 162.26 | H-Bond (Ligand Donor) |
| C16 | CB | ALA- 28 | 4.2 | 0 | Hydrophobic |
| C25 | CB | ALA- 28 | 4.06 | 0 | Hydrophobic |
| C3 | CB | ALA- 28 | 3.34 | 0 | Hydrophobic |
| O26 | N | ASP- 29 | 3.05 | 125.65 | H-Bond (Protein Donor) |
| O28 | N | ASP- 29 | 3 | 161.48 | H-Bond (Protein Donor) |
| C27 | CB | ASP- 29 | 3.83 | 0 | Hydrophobic |
| C40 | CB | ASP- 29 | 3.89 | 0 | Hydrophobic |
| O26 | N | ASN- 30 | 3.36 | 172.22 | H-Bond (Protein Donor) |
| O39 | N | ASN- 30 | 3.14 | 138.74 | H-Bond (Protein Donor) |
| C40 | CB | ASN- 30 | 3.98 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 32 | 3.81 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 32 | 3.68 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 47 | 4.36 | 0 | Hydrophobic |
| C7 | CB | VAL- 47 | 4.12 | 0 | Hydrophobic |
| C31 | CB | VAL- 47 | 4.3 | 0 | Hydrophobic |
| C40 | CG1 | VAL- 47 | 3.67 | 0 | Hydrophobic |
| C5 | CG1 | ILE- 50 | 4.35 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 50 | 4.28 | 0 | Hydrophobic |
| C14 | CB | ILE- 50 | 4.3 | 0 | Hydrophobic |
| C37 | CG2 | ILE- 50 | 4.06 | 0 | Hydrophobic |
| C35 | CB | PRO- 81 | 4.04 | 0 | Hydrophobic |
| C36 | CG | PRO- 81 | 3.95 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 82 | 3.69 | 0 | Hydrophobic |
| C34 | CB | VAL- 82 | 3.76 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 82 | 3.24 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 84 | 4.38 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 84 | 4.04 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 84 | 4.2 | 0 | Hydrophobic |
