sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2004-03-04
| Name: | Nogalonic acid methyl ester cyclase |
|---|---|
| ID: | Q9RN59_STRNO |
| AC: | Q9RN59 |
| Organism: | Streptomyces nogalater |
| Reign: | Bacteria |
| TaxID: | 38314 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.765 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.453 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 79.70 | 20.30 |
| According to VolSite | |
| HET Code: | NGV |
|---|---|
| Formula: | C21H12O7 |
| Molecular weight: | 376.316 g/mol |
| DrugBank ID: | DB04064 |
| Buried Surface Area: | 64.14 % |
| Polar Surface area: | 123.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 7.54339 | -1.15836 | 14.2548 |
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 |
| C15 | CD1 | PHE- 15 | 4.34 | 0 | Hydrophobic |
| C13 | CZ | PHE- 15 | 3.98 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 51 | 3.68 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 51 | 3.43 | 0 | Hydrophobic |
| C20 | CZ3 | TRP- 54 | 3.49 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 55 | 4.02 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 55 | 4.01 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 65 | 3.94 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 83 | 4.47 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 91 | 3.81 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 91 | 3.64 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 92 | 4.48 | 0 | Hydrophobic |
| O17 | NE2 | GLN- 105 | 2.53 | 165.16 | H-Bond (Protein Donor) |
| C11 | CG | PRO- 123 | 3.61 | 0 | Hydrophobic |
| C16 | CD2 | PHE- 125 | 3.47 | 0 | Hydrophobic |
| C1 | CG2 | THR- 128 | 3.77 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 129 | 4.18 | 0 | Hydrophobic |
