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
2011-03-09
| Name: | Pol protein |
|---|---|
| ID: | Q000H7_9HIV1 |
| AC: | Q000H7 |
| Organism: | Human immunodeficiency virus 1 |
| Reign: | Viruses |
| TaxID: | 11676 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 51 % |
| B | 49 % |
| B-Factor: | 22.818 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.336 | 290.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.86 | 58.14 |
| According to VolSite | |
| HET Code: | RSY |
|---|---|
| Formula: | C31H43ClN6O6 |
| Molecular weight: | 631.163 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 37.45 % |
| Polar Surface area: | 192.6 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 17 |
| X | Y | Z |
|---|---|---|
| 14.3582 | 8.31957 | 0.263841 |
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 |
| O20 | ND2 | ASN- 25 | 3.25 | 144.99 | H-Bond (Protein Donor) |
| O20 | ND2 | ASN- 25 | 3.07 | 142.28 | H-Bond (Protein Donor) |
| O17 | ND2 | ASN- 25 | 3.34 | 122.31 | H-Bond (Protein Donor) |
| C42 | CG2 | VAL- 32 | 3.45 | 0 | Hydrophobic |
| C41 | CB | VAL- 32 | 3.9 | 0 | Hydrophobic |
| C02 | CB | ILE- 50 | 4.24 | 0 | Hydrophobic |
| C01 | CD1 | ILE- 50 | 4.22 | 0 | Hydrophobic |
| C03 | CD1 | ILE- 50 | 3.69 | 0 | Hydrophobic |
| C41 | CB | THR- 80 | 4.24 | 0 | Hydrophobic |
| C25 | CB | PRO- 81 | 3.78 | 0 | Hydrophobic |
| C26 | CG | PRO- 81 | 3.88 | 0 | Hydrophobic |
| C25 | CG2 | THR- 82 | 3.26 | 0 | Hydrophobic |
| C26 | CG2 | THR- 82 | 3.65 | 0 | Hydrophobic |
| C42 | CB | VAL- 84 | 3.75 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 84 | 3.45 | 0 | Hydrophobic |
