sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2006-07-17
| Name: | AppA, antirepressor of ppsR, sensor of blue light |
|---|---|
| ID: | Q3J677_RHOS4 |
| AC: | Q3J677 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 272943 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 48.944 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.612 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.29 | 42.71 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 62.33 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 28.4123 | 47.3149 | 7.29645 |
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 |
| C7M | CZ | TYR- 21 | 4.43 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 37 | 3.61 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 37 | 3.48 | 0 | Hydrophobic |
| C4' | CG2 | THR- 40 | 3.97 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 45 | 2.9 | 169.36 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 45 | 3.38 | 164.28 | H-Bond (Protein Donor) |
| C6 | CG | LEU- 54 | 4.28 | 0 | Hydrophobic |
| C7M | CD2 | LEU- 54 | 4.2 | 0 | Hydrophobic |
| C7M | CG | PHE- 61 | 3.65 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 63 | 2.71 | 143.76 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 63 | 3.46 | 131.27 | H-Bond (Protein Donor) |
| C5' | CB | HIS- 78 | 4.06 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 79 | 4.42 | 0 | Hydrophobic |
| C9A | CG1 | ILE- 79 | 3.64 | 0 | Hydrophobic |
| C2' | CG1 | ILE- 79 | 4.03 | 0 | Hydrophobic |
| C8M | CB | ASP- 82 | 4.21 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 82 | 3.03 | 172.9 | H-Bond (Ligand Donor) |
| C8M | CB | ARG- 84 | 4.08 | 0 | Hydrophobic |
