sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-08-05
| Name: | Uncharacterized protein |
|---|---|
| ID: | Q6N6X2_RHOPA |
| AC: | Q6N6X2 |
| Organism: | Rhodopseudomonas palustris |
| Reign: | Bacteria |
| TaxID: | 258594 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 8.398 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 41 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.811 | 627.750 |
| % Hydrophobic | % Polar |
|---|---|
| 52.15 | 47.85 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 74.98 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -6.05163 | 48.1358 | 9.33422 |
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 |
| C2' | CD2 | TYR- 17 | 3.56 | 0 | Hydrophobic |
| C3' | CZ | TYR- 17 | 4 | 0 | Hydrophobic |
| SD | CZ | TYR- 17 | 3.63 | 0 | Hydrophobic |
| O | OH | TYR- 24 | 3.5 | 141.02 | H-Bond (Protein Donor) |
| CB | CE1 | TYR- 24 | 4.24 | 0 | Hydrophobic |
| CE | CZ | TYR- 24 | 4.05 | 0 | Hydrophobic |
| SD | CZ | TYR- 24 | 3.66 | 0 | Hydrophobic |
| N | O | GLY- 51 | 2.92 | 168.51 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 72 | 2.69 | 160.75 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 72 | 2.69 | 150.25 | H-Bond (Ligand Donor) |
| N3 | N | GLY- 73 | 2.94 | 125.59 | H-Bond (Protein Donor) |
| C3' | CD1 | LEU- 77 | 3.98 | 0 | Hydrophobic |
| N1 | N | PHE- 94 | 3.14 | 152.08 | H-Bond (Protein Donor) |
| DuAr | DuAr | PHE- 94 | 3.61 | 0 | Aromatic Face/Face |
| N | O | HIS- 109 | 2.85 | 163.79 | H-Bond (Ligand Donor) |
| CG | CB | ALA- 110 | 4.41 | 0 | Hydrophobic |
| CE | CB | ALA- 110 | 4.4 | 0 | Hydrophobic |
| C4' | CB | CYS- 111 | 3.82 | 0 | Hydrophobic |
| N | O | HOH- 230 | 2.64 | 159.82 | H-Bond (Ligand Donor) |
| N6 | O | HOH- 247 | 3.14 | 162.07 | H-Bond (Ligand Donor) |
