sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2005-06-30
| Name: | 6,7-dimethyl-8-ribityllumazine synthase |
|---|---|
| ID: | RIB4_SCHPO |
| AC: | Q9UUB1 |
| Organism: | Schizosaccharomyces pombe |
| Reign: | Eukaryota |
| TaxID: | 284812 |
| EC Number: | 2.5.1.78 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 36 % |
| D | 64 % |
| B-Factor: | 42.482 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.745 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.00 | 56.00 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 60.23 % |
| 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 |
|---|---|---|
| 60.6386 | 36.6274 | 8.74085 |
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 |
| C1' | CE1 | TYR- 27 | 4.11 | 0 | Hydrophobic |
| O2 | N | SER- 62 | 3.1 | 162.12 | H-Bond (Protein Donor) |
| O2' | N | TRP- 63 | 3.2 | 159.65 | H-Bond (Protein Donor) |
| C3' | CB | TRP- 63 | 3.28 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 64 | 3.32 | 160.12 | H-Bond (Ligand Donor) |
| O3' | OE1 | GLU- 64 | 2.96 | 135.08 | H-Bond (Ligand Donor) |
| O5' | OE2 | GLU- 64 | 2.84 | 130.6 | H-Bond (Ligand Donor) |
| N3 | O | VAL- 86 | 3.03 | 169.3 | H-Bond (Ligand Donor) |
| O4 | N | ILE- 88 | 3.35 | 168.21 | H-Bond (Protein Donor) |
| C5' | CG2 | ILE- 118 | 3.87 | 0 | Hydrophobic |
| O4' | O | LEU- 119 | 3.03 | 154.82 | H-Bond (Ligand Donor) |
| C7M | CD | ARG- 133 | 4.37 | 0 | Hydrophobic |
| C8M | CB | HIS- 142 | 4.15 | 0 | Hydrophobic |
| C8M | CZ2 | TRP- 146 | 4.11 | 0 | Hydrophobic |
