sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2008-09-19
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1A2 |
| AC: | P03369 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11685 |
| EC Number: | 3.4.23.16 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 52 % |
| B | 48 % |
| B-Factor: | 25.872 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.840 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.21 | 54.79 |
| According to VolSite | |
| HET Code: | DR7 |
|---|---|
| Formula: | C38H52N6O7 |
| Molecular weight: | 704.855 g/mol |
| DrugBank ID: | DB01072 |
| Buried Surface Area: | 63.53 % |
| Polar Surface area: | 171.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 20.4266 | 32.0751 | 14.4066 |
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 |
| NBD | NH1 | ARG- 8 | 3.32 | 158.72 | H-Bond (Protein Donor) |
| CBA | CD2 | LEU- 23 | 4.44 | 0 | Hydrophobic |
| CAT | CD2 | LEU- 23 | 4.41 | 0 | Hydrophobic |
| CAX | CD2 | LEU- 23 | 4.25 | 0 | Hydrophobic |
| OAM | OD1 | ASP- 25 | 2.75 | 141.88 | H-Bond (Ligand Donor) |
| OAM | OD2 | ASP- 25 | 2.89 | 148.97 | H-Bond (Ligand Donor) |
| NBG | O | GLY- 27 | 3.27 | 147.83 | H-Bond (Ligand Donor) |
| NBH | O | GLY- 27 | 3.26 | 172.13 | H-Bond (Ligand Donor) |
| CG1 | CB | ALA- 28 | 3.48 | 0 | Hydrophobic |
| CAF | CB | ALA- 28 | 4.05 | 0 | Hydrophobic |
| CAA | CB | ASP- 29 | 4.16 | 0 | Hydrophobic |
| CAB | CB | ASP- 29 | 4.47 | 0 | Hydrophobic |
| OAI | N | ASP- 29 | 3.03 | 165.75 | H-Bond (Protein Donor) |
| OAJ | N | ASP- 29 | 2.9 | 177.66 | H-Bond (Protein Donor) |
| CG2 | CB | ASP- 30 | 4.21 | 0 | Hydrophobic |
| CAG | CB | ASP- 30 | 4.33 | 0 | Hydrophobic |
| CAE | CG2 | VAL- 32 | 4.26 | 0 | Hydrophobic |
| CG2 | CG2 | VAL- 32 | 4.47 | 0 | Hydrophobic |
| CG1 | CG2 | VAL- 32 | 4.43 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 32 | 4.3 | 0 | Hydrophobic |
| CAG | CG2 | VAL- 32 | 4.18 | 0 | Hydrophobic |
| CAE | CD1 | ILE- 47 | 3.76 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 47 | 4.11 | 0 | Hydrophobic |
| N | O | GLY- 48 | 3.03 | 162.34 | H-Bond (Ligand Donor) |
| NBF | O | GLY- 48 | 3.12 | 152.33 | H-Bond (Ligand Donor) |
| CAE | CG1 | ILE- 50 | 3.68 | 0 | Hydrophobic |
| CG1 | CG1 | ILE- 50 | 4.31 | 0 | Hydrophobic |
| CBB | CG1 | ILE- 50 | 4.49 | 0 | Hydrophobic |
| CAU | CG1 | ILE- 50 | 3.81 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 50 | 3.41 | 0 | Hydrophobic |
| CAV | CG | PRO- 81 | 4.04 | 0 | Hydrophobic |
| CAN | CG | PRO- 81 | 3.77 | 0 | Hydrophobic |
| CAY | CG | PRO- 81 | 3.48 | 0 | Hydrophobic |
| CAZ | CG1 | VAL- 82 | 3.83 | 0 | Hydrophobic |
| CAN | CG1 | VAL- 82 | 3.91 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 84 | 3.97 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 84 | 3.84 | 0 | Hydrophobic |
| CAU | CD1 | ILE- 84 | 3.9 | 0 | Hydrophobic |
| CBB | CD1 | ILE- 84 | 3.68 | 0 | Hydrophobic |
| OBJ | O | HOH- 508 | 3.4 | 125.46 | H-Bond (Protein Donor) |
| OBI | O | HOH- 558 | 3.43 | 120.73 | H-Bond (Protein Donor) |
