sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.390 Å
X-ray
2009-10-06
| 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 |
|---|---|
| C | 48 % |
| D | 52 % |
| B-Factor: | 17.459 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.192 | 951.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.04 | 54.96 |
| According to VolSite | |
| HET Code: | ROC |
|---|---|
| Formula: | C38H51N6O5 |
| Molecular weight: | 671.849 g/mol |
| DrugBank ID: | DB01232 |
| Buried Surface Area: | 70.6 % |
| 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 |
|---|---|---|
| 5.23908 | 13.3047 | -0.296857 |
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 | 4.35 | 0 | Hydrophobic |
| CD2 | CD2 | LEU- 23 | 3.63 | 0 | Hydrophobic |
| O2 | OD2 | ASP- 25 | 2.63 | 158.4 | H-Bond (Ligand Donor) |
| O2 | OD1 | ASP- 25 | 2.58 | 154.06 | H-Bond (Protein Donor) |
| N2 | O | GLY- 27 | 3.22 | 159.74 | H-Bond (Ligand Donor) |
| CB | CB | ALA- 28 | 4.28 | 0 | Hydrophobic |
| C11 | CB | ALA- 28 | 4.23 | 0 | Hydrophobic |
| C32 | CB | ALA- 28 | 4.16 | 0 | Hydrophobic |
| O | N | ASP- 29 | 3.05 | 156.37 | H-Bond (Protein Donor) |
| OD1 | N | ASP- 30 | 2.98 | 151.25 | H-Bond (Protein Donor) |
| ND2 | OD2 | ASP- 30 | 3.27 | 146.54 | H-Bond (Ligand Donor) |
| C11 | CB | ASP- 30 | 3.96 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 32 | 3.85 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 32 | 4.5 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 32 | 3.91 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 47 | 4.33 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 47 | 3.66 | 0 | Hydrophobic |
| N | O | GLY- 48 | 2.92 | 141.17 | H-Bond (Ligand Donor) |
| ND2 | O | GLY- 48 | 3.27 | 148.35 | H-Bond (Ligand Donor) |
| CB | CD1 | ILE- 50 | 4.01 | 0 | Hydrophobic |
| C61 | CG1 | ILE- 50 | 3.94 | 0 | Hydrophobic |
| C71 | CB | ILE- 50 | 4.2 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 50 | 3.51 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 50 | 3.32 | 0 | Hydrophobic |
| CD1 | CG1 | ILE- 50 | 3.89 | 0 | Hydrophobic |
| C51 | CG | PRO- 81 | 3.71 | 0 | Hydrophobic |
| C6 | CB | PRO- 81 | 3.57 | 0 | Hydrophobic |
| C7 | CG | PRO- 81 | 3.57 | 0 | Hydrophobic |
| CZ | CG | PRO- 81 | 4.08 | 0 | Hydrophobic |
| CE2 | CB | VAL- 82 | 4.04 | 0 | Hydrophobic |
| CZ | CG2 | VAL- 82 | 3.94 | 0 | Hydrophobic |
| C41 | CG2 | VAL- 82 | 3.92 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 82 | 4.22 | 0 | Hydrophobic |
| C51 | CB | VAL- 82 | 4.27 | 0 | Hydrophobic |
| CB | CD1 | ILE- 84 | 4.27 | 0 | Hydrophobic |
| C32 | CD1 | ILE- 84 | 3.61 | 0 | Hydrophobic |
| C7A | CG2 | ILE- 84 | 3.9 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 84 | 3.54 | 0 | Hydrophobic |
