sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2015-06-05
| Name: | Uncharacterized protein |
|---|---|
| ID: | C7Q5P8_CATAD |
| AC: | C7Q5P8 |
| Organism: | Catenulispora acidiphila |
| Reign: | Bacteria |
| TaxID: | 479433 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 53.503 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.093 | 408.375 |
| % Hydrophobic | % Polar |
|---|---|
| 42.98 | 57.02 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 71.54 % |
| 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 |
|---|---|---|
| -7.65274 | -18.2696 | 47.4267 |
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 |
| N | O | GLY- 38 | 3.06 | 154.27 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 61 | 2.82 | 178.91 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 61 | 2.73 | 155.93 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 61 | 3.45 | 146.6 | H-Bond (Ligand Donor) |
| O3' | NH1 | ARG- 66 | 3.35 | 133.37 | H-Bond (Protein Donor) |
| N1 | N | ILE- 93 | 3.04 | 156.02 | H-Bond (Protein Donor) |
| N6 | OE1 | GLU- 94 | 2.99 | 165.93 | H-Bond (Ligand Donor) |
| N | O | LEU- 110 | 2.88 | 150.32 | H-Bond (Ligand Donor) |
| CB | CB | MET- 111 | 4.41 | 0 | Hydrophobic |
| CE | CE2 | TRP- 113 | 3.51 | 0 | Hydrophobic |
| N7 | N | LEU- 116 | 3.35 | 147.05 | H-Bond (Protein Donor) |
| OXT | OG | SER- 201 | 2.59 | 169.53 | H-Bond (Protein Donor) |
| CE | CB | ALA- 204 | 4.15 | 0 | Hydrophobic |
