sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.220 Å
X-ray
2005-10-11
| Name: | Riboflavin synthase |
|---|---|
| ID: | RISC_METJA |
| AC: | Q58584 |
| Organism: | Methanocaldococcus jannaschii |
| Reign: | Archaea |
| TaxID: | 243232 |
| EC Number: | 2.5.1.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 55 % |
| E | 45 % |
| B-Factor: | 34.883 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.956 | 1117.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.92 | 54.08 |
| According to VolSite | |
| HET Code: | RDL |
|---|---|
| Formula: | C11H14N4O8 |
| Molecular weight: | 330.251 g/mol |
| DrugBank ID: | DB02214 |
| Buried Surface Area: | 44.29 % |
| Polar Surface area: | 188.52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 7 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -13.142 | 3.50365 | -19.0907 |
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 | CZ | PHE- 12 | 3.56 | 0 | Hydrophobic |
| O15 | OD2 | ASP- 73 | 3.36 | 142.91 | H-Bond (Ligand Donor) |
| O14 | OD1 | ASP- 73 | 3.02 | 160.47 | H-Bond (Ligand Donor) |
| O4 | NE2 | HIS- 122 | 2.53 | 168.52 | H-Bond (Protein Donor) |
