sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2011-07-31
| Name: | Uncharacterized protein |
|---|---|
| ID: | A6L5C0_BACV8 |
| AC: | A6L5C0 |
| Organism: | Bacteroides vulgatus |
| Reign: | Bacteria |
| TaxID: | 435590 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 37.195 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.691 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.34 | 62.66 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 67.53 % |
| 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 |
|---|---|---|
| -45.682 | 21.1692 | 24.9429 |
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 |
| O | NE | ARG- 25 | 3.45 | 138.87 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 25 | 2.98 | 163.13 | H-Bond (Protein Donor) |
| OXT | NE | ARG- 25 | 3.03 | 166.08 | H-Bond (Protein Donor) |
| O | CZ | ARG- 25 | 3.66 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 25 | 3.98 | 0 | Ionic (Protein Cationic) |
| OXT | N | GLN- 26 | 2.85 | 153.75 | H-Bond (Protein Donor) |
| SD | CB | GLN- 26 | 3.81 | 0 | Hydrophobic |
| CB | CB | GLN- 26 | 3.78 | 0 | Hydrophobic |
| N | O | GLY- 54 | 2.75 | 160.31 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 76 | 2.58 | 156.42 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 76 | 2.96 | 166.7 | H-Bond (Ligand Donor) |
| N3 | N | PHE- 77 | 3.39 | 138.4 | H-Bond (Protein Donor) |
| C3' | CE2 | PHE- 81 | 3.91 | 0 | Hydrophobic |
| N6 | OG | SER- 104 | 3.16 | 155.75 | H-Bond (Ligand Donor) |
| N1 | N | MET- 105 | 3 | 157.88 | H-Bond (Protein Donor) |
| N | O | GLU- 121 | 2.78 | 155.72 | H-Bond (Ligand Donor) |
| C5' | CB | ALA- 123 | 3.88 | 0 | Hydrophobic |
