sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2010-09-22
| 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 | 2 % |
| C | 48 % |
| D | 50 % |
| B-Factor: | 23.042 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.930 | 850.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.05 | 55.95 |
| According to VolSite | |
| HET Code: | DR7 |
|---|---|
| Formula: | C38H52N6O7 |
| Molecular weight: | 704.855 g/mol |
| DrugBank ID: | DB01072 |
| Buried Surface Area: | 62.68 % |
| 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 |
|---|---|---|
| 5.24773 | 14.5516 | 1.44639 |
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 |
| CAX | CD2 | LEU- 23 | 3.93 | 0 | Hydrophobic |
| CAU | CD2 | LEU- 23 | 3.88 | 0 | Hydrophobic |
| OAM | OD1 | ASP- 25 | 2.74 | 134.39 | H-Bond (Ligand Donor) |
| OAM | OD1 | ASP- 25 | 2.77 | 152.66 | H-Bond (Protein Donor) |
| NBG | O | GLY- 27 | 3.09 | 155.2 | H-Bond (Ligand Donor) |
| NBH | O | GLY- 27 | 3.05 | 161.18 | H-Bond (Ligand Donor) |
| CG1 | CB | ALA- 28 | 3.98 | 0 | Hydrophobic |
| CAF | CB | ALA- 28 | 3.92 | 0 | Hydrophobic |
| CAA | CB | ASP- 29 | 4.44 | 0 | Hydrophobic |
| CAB | CB | ASP- 29 | 4.33 | 0 | Hydrophobic |
| OAI | N | ASP- 29 | 2.98 | 168.69 | H-Bond (Protein Donor) |
| OAJ | N | ASP- 29 | 2.93 | 168.09 | H-Bond (Protein Donor) |
| CAE | CB | ASP- 30 | 4.35 | 0 | Hydrophobic |
| CAG | CB | ASP- 30 | 4.37 | 0 | Hydrophobic |
| CAE | CG2 | VAL- 32 | 4.15 | 0 | Hydrophobic |
| CG1 | CG2 | VAL- 32 | 4.33 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 32 | 4.28 | 0 | Hydrophobic |
| CAE | CD1 | ILE- 47 | 4.35 | 0 | Hydrophobic |
| CG2 | CD1 | ILE- 47 | 3.97 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 47 | 3.83 | 0 | Hydrophobic |
| CAG | CD1 | ILE- 47 | 4.18 | 0 | Hydrophobic |
| N | O | GLY- 48 | 2.93 | 164.94 | H-Bond (Ligand Donor) |
| NBF | O | GLY- 48 | 2.96 | 166.06 | H-Bond (Ligand Donor) |
| CG2 | CG2 | VAL- 50 | 3.6 | 0 | Hydrophobic |
| CAT | CG2 | VAL- 50 | 4.19 | 0 | Hydrophobic |
| CAH | CB | VAL- 50 | 3.99 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 50 | 4.21 | 0 | Hydrophobic |
| CAW | CG1 | VAL- 50 | 4.19 | 0 | Hydrophobic |
| CG1 | CG1 | VAL- 50 | 3.82 | 0 | Hydrophobic |
| CAP | CG | PRO- 81 | 3.62 | 0 | Hydrophobic |
| CAY | CB | PRO- 81 | 3.99 | 0 | Hydrophobic |
| CAX | CG1 | VAL- 82 | 3.87 | 0 | Hydrophobic |
| CAN | CG2 | VAL- 82 | 3.86 | 0 | Hydrophobic |
| CG1 | CG1 | ILE- 84 | 4.04 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 84 | 3.53 | 0 | Hydrophobic |
| CBA | CD1 | ILE- 84 | 3.71 | 0 | Hydrophobic |
