sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2005-08-18
| 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 | 48 % |
| B | 52 % |
| B-Factor: | 25.814 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.963 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 43.73 | 56.27 |
| According to VolSite | |
| HET Code: | DR7 |
|---|---|
| Formula: | C38H52N6O7 |
| Molecular weight: | 704.855 g/mol |
| DrugBank ID: | DB01072 |
| Buried Surface Area: | 62.39 % |
| 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 |
|---|---|---|
| -39.2371 | 69.5778 | 28.0199 |
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 |
| CAU | CD2 | LEU- 23 | 4.47 | 0 | Hydrophobic |
| CAW | CD2 | LEU- 23 | 4.38 | 0 | Hydrophobic |
| OAM | OD1 | ASP- 25 | 2.74 | 167.45 | H-Bond (Ligand Donor) |
| NBG | O | GLY- 27 | 3.09 | 152.42 | H-Bond (Ligand Donor) |
| NBH | O | GLY- 27 | 3.08 | 144.28 | H-Bond (Ligand Donor) |
| CG1 | CB | ALA- 28 | 3.9 | 0 | Hydrophobic |
| CAF | CB | ALA- 28 | 3.94 | 0 | Hydrophobic |
| CAA | CB | ASP- 29 | 4.38 | 0 | Hydrophobic |
| CAB | CB | ASP- 29 | 4.43 | 0 | Hydrophobic |
| OAI | N | ASP- 29 | 3.16 | 177.32 | H-Bond (Protein Donor) |
| OAJ | N | ASP- 29 | 3.04 | 177.34 | H-Bond (Protein Donor) |
| CG2 | CB | ASP- 30 | 4.39 | 0 | Hydrophobic |
| CAH | CB | ASP- 30 | 4.11 | 0 | Hydrophobic |
| CG2 | CG2 | VAL- 32 | 4.14 | 0 | Hydrophobic |
| CG1 | CG2 | VAL- 32 | 4.35 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 32 | 4.17 | 0 | Hydrophobic |
| CAE | CD1 | ILE- 47 | 4.34 | 0 | Hydrophobic |
| CAG | CD1 | ILE- 47 | 4.15 | 0 | Hydrophobic |
| N | O | GLY- 48 | 2.76 | 137.43 | H-Bond (Ligand Donor) |
| NBF | O | GLY- 48 | 3 | 160.86 | H-Bond (Ligand Donor) |
| CAE | CG2 | ILE- 50 | 3.81 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 50 | 4.14 | 0 | Hydrophobic |
| CAG | CG2 | ILE- 50 | 3.78 | 0 | Hydrophobic |
| CAX | CD1 | ILE- 50 | 4.16 | 0 | Hydrophobic |
| CAZ | CG | PRO- 81 | 4.23 | 0 | Hydrophobic |
| CBQ | CB | PRO- 81 | 4.35 | 0 | Hydrophobic |
| CAO | CB | PRO- 81 | 3.98 | 0 | Hydrophobic |
| CAP | CG | PRO- 81 | 4.04 | 0 | Hydrophobic |
| CAV | CG | PRO- 81 | 3.27 | 0 | Hydrophobic |
| CAY | CG1 | VAL- 82 | 3.73 | 0 | Hydrophobic |
| CAN | CG1 | VAL- 82 | 3.87 | 0 | Hydrophobic |
| CG1 | CD1 | ILE- 84 | 3.59 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 84 | 3.68 | 0 | Hydrophobic |
| CBA | CD1 | ILE- 84 | 3.96 | 0 | Hydrophobic |
| CBB | CD1 | ILE- 84 | 3.69 | 0 | Hydrophobic |
