sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.720 Å
X-ray
2008-06-16
| Name: | Uncharacterized protein |
|---|---|
| ID: | O67440_AQUAE |
| AC: | O67440 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 26.221 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.507 | 756.000 |
| % Hydrophobic | % Polar |
|---|---|
| 46.88 | 53.13 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 79.12 % |
| 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 |
|---|---|---|
| 24.6129 | 1.18722 | 25.8366 |
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 |
| N7 | NZ | LYS- 6 | 2.9 | 167.46 | H-Bond (Protein Donor) |
| SD | CB | PHE- 7 | 4.23 | 0 | Hydrophobic |
| CE | CD1 | PHE- 7 | 4.3 | 0 | Hydrophobic |
| C3' | CB | PHE- 7 | 3.74 | 0 | Hydrophobic |
| CB | CD2 | LEU- 15 | 3.57 | 0 | Hydrophobic |
| SD | CD2 | LEU- 15 | 4.24 | 0 | Hydrophobic |
| O | CZ | ARG- 20 | 3.94 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 20 | 3.63 | 0 | Ionic (Protein Cationic) |
| O | NH2 | ARG- 20 | 3.1 | 149.76 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 20 | 2.99 | 161.16 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 20 | 3.36 | 139.3 | H-Bond (Protein Donor) |
| N | O | GLY- 45 | 2.83 | 150.61 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 69 | 3.24 | 173.89 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 69 | 2.54 | 137.22 | H-Bond (Ligand Donor) |
| C2' | CG2 | VAL- 70 | 4.26 | 0 | Hydrophobic |
| O2' | NE2 | GLN- 71 | 3.15 | 167.28 | H-Bond (Protein Donor) |
| C3' | CE | MET- 74 | 4.35 | 0 | Hydrophobic |
| N6 | OE2 | GLU- 97 | 3.18 | 140.44 | H-Bond (Ligand Donor) |
| N6 | O | GLU- 97 | 3.08 | 144.25 | H-Bond (Ligand Donor) |
| N | O | ALA- 113 | 2.77 | 131.79 | H-Bond (Ligand Donor) |
| CE | CB | PHE- 114 | 3.84 | 0 | Hydrophobic |
| O4' | OG1 | THR- 115 | 3.43 | 149.9 | H-Bond (Protein Donor) |
| C5' | CB | THR- 115 | 3.95 | 0 | Hydrophobic |
| OXT | O | HOH- 221 | 2.51 | 152.97 | H-Bond (Protein Donor) |
