sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2003-06-06
| Name: | Riboflavin synthase |
|---|---|
| ID: | RISA_ECOLI |
| AC: | P0AFU8 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 2.5.1.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 79 % |
| B | 21 % |
| B-Factor: | 36.209 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.048 | 236.250 |
| % Hydrophobic | % Polar |
|---|---|
| 31.43 | 68.57 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 56.9 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 21.9453 | 26.3383 | 40.419 |
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 |
| C8M | CE | MET- 1 | 4.43 | 0 | Hydrophobic |
| O4' | O | GLY- 4 | 3 | 120.34 | H-Bond (Ligand Donor) |
| C8M | CD1 | ILE- 5 | 4.02 | 0 | Hydrophobic |
| O4' | N | VAL- 6 | 2.93 | 154.63 | H-Bond (Protein Donor) |
| C5' | CB | VAL- 6 | 4.39 | 0 | Hydrophobic |
| O5' | O | VAL- 6 | 2.96 | 166.76 | H-Bond (Ligand Donor) |
| C2' | SG | CYS- 47 | 4.14 | 0 | Hydrophobic |
| C4' | SG | CYS- 47 | 3.83 | 0 | Hydrophobic |
| O2' | O | CYS- 48 | 2.8 | 169.72 | H-Bond (Ligand Donor) |
| C7 | SG | CYS- 48 | 3.56 | 0 | Hydrophobic |
| C8 | SG | CYS- 48 | 3.87 | 0 | Hydrophobic |
| C9 | CB | CYS- 48 | 4.11 | 0 | Hydrophobic |
| O4 | N | THR- 50 | 2.95 | 168.37 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 50 | 3.1 | 157.94 | H-Bond (Protein Donor) |
| N3 | O | ASP- 62 | 2.72 | 167.62 | H-Bond (Ligand Donor) |
| O2 | N | MET- 64 | 2.98 | 161.98 | H-Bond (Protein Donor) |
| N1 | OG1 | THR- 67 | 3.06 | 142.44 | H-Bond (Protein Donor) |
| O2 | OG1 | THR- 67 | 2.64 | 137.44 | H-Bond (Protein Donor) |
| O3' | OG1 | THR- 67 | 2.85 | 162.42 | H-Bond (Ligand Donor) |
| C4' | CG2 | THR- 67 | 4.45 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 70 | 3.94 | 0 | Hydrophobic |
| C5' | CG2 | THR- 71 | 3.88 | 0 | Hydrophobic |
| O4 | O | HOH- 101 | 2.72 | 179.97 | H-Bond (Protein Donor) |
