sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
2005-08-30
| Name: | Regulatory protein SdiA |
|---|---|
| ID: | SDIA_ECOLI |
| AC: | P07026 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.949 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.329 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 65.77 | 34.23 |
| According to VolSite | |
| HET Code: | HTF |
|---|---|
| Formula: | C12H21NO3 |
| Molecular weight: | 227.300 g/mol |
| DrugBank ID: | DB07928 |
| Buried Surface Area: | 72.97 % |
| Polar Surface area: | 55.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.911813 | -5.90262 | -7.10506 |
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 |
| C4 | CB | SER- 43 | 3.94 | 0 | Hydrophobic |
| C8 | CE1 | PHE- 59 | 3.71 | 0 | Hydrophobic |
| C7 | CD1 | PHE- 59 | 4.3 | 0 | Hydrophobic |
| C6 | CG | PHE- 59 | 3.82 | 0 | Hydrophobic |
| C5 | CB | PHE- 59 | 4.21 | 0 | Hydrophobic |
| C7 | CG2 | THR- 61 | 4.09 | 0 | Hydrophobic |
| C5 | CG2 | THR- 61 | 4.09 | 0 | Hydrophobic |
| C7 | CD2 | TYR- 63 | 4.43 | 0 | Hydrophobic |
| C5 | CE2 | TYR- 63 | 4.08 | 0 | Hydrophobic |
| C3 | CE2 | TYR- 63 | 4.08 | 0 | Hydrophobic |
| O1 | NE1 | TRP- 67 | 2.96 | 146.83 | H-Bond (Protein Donor) |
| CB | CZ2 | TRP- 67 | 3.76 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 68 | 4.11 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 71 | 4.17 | 0 | Hydrophobic |
| C2 | CZ | TYR- 71 | 3.55 | 0 | Hydrophobic |
| C8 | CD1 | TYR- 71 | 3.52 | 0 | Hydrophobic |
| C8 | CG | GLN- 72 | 4.16 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 82 | 4.29 | 0 | Hydrophobic |
| CG | CH2 | TRP- 95 | 3.34 | 0 | Hydrophobic |
| CG | CE2 | PHE- 100 | 4.25 | 0 | Hydrophobic |
| CG | CB | ALA- 110 | 3.54 | 0 | Hydrophobic |
| CB | CD2 | LEU- 115 | 3.57 | 0 | Hydrophobic |
