sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2007-04-27
| Name: | 1,4-dihydroxy-2-naphthoyl-CoA synthase |
|---|---|
| ID: | MENB_STAAC |
| AC: | Q5HH38 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 93062 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 88 % |
| B | 12 % |
| B-Factor: | 30.777 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.143 | 1046.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.39 | 51.61 |
| According to VolSite | |
| HET Code: | CAA |
|---|---|
| Formula: | C25H36N7O18P3S |
| Molecular weight: | 847.576 g/mol |
| DrugBank ID: | DB03059 |
| Buried Surface Area: | 35.88 % |
| Polar Surface area: | 446.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 23 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 22 |
| X | Y | Z |
|---|---|---|
| 8.16963 | -19.7564 | -33.5268 |
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 |
| C1B | CG2 | VAL- 33 | 4.25 | 0 | Hydrophobic |
| O3A | NH2 | ARG- 34 | 2.87 | 129.24 | H-Bond (Protein Donor) |
| O5A | NH2 | ARG- 34 | 3.37 | 150.54 | H-Bond (Protein Donor) |
| S1P | CZ | PHE- 37 | 4.42 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 94 | 3.74 | 0 | Hydrophobic |
| C6P | CB | THR- 143 | 4.21 | 0 | Hydrophobic |
| CEP | CE2 | PHE- 258 | 3.71 | 0 | Hydrophobic |
