sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
1996-01-16
| 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: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 49 % |
| B | 51 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 45 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.451 | 783.000 |
| % Hydrophobic | % Polar |
|---|---|
| 59.05 | 40.95 |
| According to VolSite | |
| HET Code: | DMP |
|---|---|
| Formula: | C35H38N2O5 |
| Molecular weight: | 566.687 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.52 % |
| Polar Surface area: | 104.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 1.32717 | -4.70002 | -5.25762 |
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 |
| C66 | CD2 | LEU- 23 | 4.03 | 0 | Hydrophobic |
| O4 | OD1 | ASP- 25 | 2.6 | 155 | H-Bond (Ligand Donor) |
| O5 | OD1 | ASP- 25 | 2.65 | 175.73 | H-Bond (Ligand Donor) |
| C26 | CB | ALA- 28 | 3.95 | 0 | Hydrophobic |
| C76 | CB | ALA- 28 | 3.75 | 0 | Hydrophobic |
| C24 | CB | ALA- 28 | 3.51 | 0 | Hydrophobic |
| C74 | CB | ALA- 28 | 3.46 | 0 | Hydrophobic |
| O27 | N | ASP- 29 | 3.09 | 161.47 | H-Bond (Protein Donor) |
| O77 | N | ASP- 29 | 2.99 | 154.51 | H-Bond (Protein Donor) |
| O77 | N | ASP- 30 | 3.46 | 147.06 | H-Bond (Protein Donor) |
| C22 | CD1 | ILE- 47 | 4.5 | 0 | Hydrophobic |
| C23 | CB | ILE- 47 | 4.06 | 0 | Hydrophobic |
| C24 | CD1 | ILE- 47 | 4.32 | 0 | Hydrophobic |
| C27 | CG2 | ILE- 47 | 4.2 | 0 | Hydrophobic |
| C72 | CD1 | ILE- 47 | 4.39 | 0 | Hydrophobic |
| C73 | CB | ILE- 47 | 4.1 | 0 | Hydrophobic |
| C74 | CD1 | ILE- 47 | 4.37 | 0 | Hydrophobic |
| C77 | CG2 | ILE- 47 | 4.42 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 50 | 3.65 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 50 | 4 | 0 | Hydrophobic |
| C72 | CD1 | ILE- 50 | 3.87 | 0 | Hydrophobic |
| C26 | CG1 | ILE- 50 | 4.28 | 0 | Hydrophobic |
| C32 | CG1 | ILE- 50 | 3.25 | 0 | Hydrophobic |
| C60 | CD1 | ILE- 50 | 3.74 | 0 | Hydrophobic |
| C62 | CG1 | ILE- 50 | 3.34 | 0 | Hydrophobic |
| C71 | CG1 | ILE- 50 | 4.23 | 0 | Hydrophobic |
| C75 | CD1 | ILE- 50 | 3.67 | 0 | Hydrophobic |
| O1 | N | ILE- 50 | 3.35 | 161.1 | H-Bond (Protein Donor) |
| O1 | N | ILE- 50 | 3.39 | 158.95 | H-Bond (Protein Donor) |
| C33 | CG | PRO- 81 | 3.65 | 0 | Hydrophobic |
| C63 | CG | PRO- 81 | 3.65 | 0 | Hydrophobic |
| C65 | CG2 | VAL- 82 | 4.47 | 0 | Hydrophobic |
| C34 | CB | VAL- 82 | 3.76 | 0 | Hydrophobic |
| C64 | CB | VAL- 82 | 3.93 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 82 | 3.94 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 84 | 4.19 | 0 | Hydrophobic |
| C75 | CG2 | ILE- 84 | 4.24 | 0 | Hydrophobic |
| C30 | CD1 | ILE- 84 | 3.45 | 0 | Hydrophobic |
| C62 | CD1 | ILE- 84 | 3.65 | 0 | Hydrophobic |
