sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2005-02-05
| Name: | AppA protein |
|---|---|
| ID: | Q53119_RHOSH |
| AC: | Q53119 |
| Organism: | Rhodobacter sphaeroides |
| Reign: | Bacteria |
| TaxID: | 1063 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 7 % |
| C | 93 % |
| B-Factor: | 77.631 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.413 | 320.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.68 | 46.32 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 62.81 % |
| 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 |
|---|---|---|
| -2.16026 | 25.2312 | 22.5287 |
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 |
| C6 | CG2 | ILE- 37 | 4.16 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 37 | 3.6 | 0 | Hydrophobic |
| C9A | CG2 | ILE- 37 | 4.1 | 0 | Hydrophobic |
| C4' | CG2 | THR- 40 | 3.69 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 45 | 2.64 | 163.63 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 45 | 2.79 | 176.42 | H-Bond (Protein Donor) |
| C6 | CD2 | LEU- 54 | 4.17 | 0 | Hydrophobic |
| C7M | CD1 | LEU- 54 | 4.29 | 0 | Hydrophobic |
| C7M | CD2 | PHE- 61 | 3.57 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 63 | 2.72 | 144.51 | H-Bond (Protein Donor) |
| N5 | NE2 | GLN- 63 | 3.42 | 138.92 | H-Bond (Protein Donor) |
| C3' | CB | HIS- 78 | 4 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 79 | 4.3 | 0 | Hydrophobic |
| C2' | CG1 | ILE- 79 | 4.22 | 0 | Hydrophobic |
| C9A | CG1 | ILE- 79 | 3.65 | 0 | Hydrophobic |
| C8M | CB | ASP- 82 | 4.09 | 0 | Hydrophobic |
| C9 | CB | ASP- 82 | 4.43 | 0 | Hydrophobic |
| C8M | CB | ARG- 84 | 4 | 0 | Hydrophobic |
