sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.240 Å
X-ray
2013-05-14
| Name: | 6,7-dimethyl-8-ribityllumazine synthase |
|---|---|
| ID: | Q6FXA8_CANGA |
| AC: | Q6FXA8 |
| Organism: | Candida glabrata |
| Reign: | Eukaryota |
| TaxID: | 284593 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 70 % |
| D | 30 % |
| B-Factor: | 14.423 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.530 | 870.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.90 | 53.10 |
| According to VolSite | |
| HET Code: | DLZ |
|---|---|
| Formula: | C13H18N4O6 |
| Molecular weight: | 326.305 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.25 % |
| Polar Surface area: | 155.04 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 4.51452 | 11.8963 | 72.7441 |
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 |
| C6 | CH2 | TRP- 27 | 3.79 | 0 | Hydrophobic |
| O2 | N | SER- 61 | 3 | 129.99 | H-Bond (Protein Donor) |
| N1 | N | SER- 61 | 3.23 | 167.68 | H-Bond (Protein Donor) |
| O2' | N | PHE- 62 | 2.97 | 169.54 | H-Bond (Protein Donor) |
| C3' | CB | PHE- 62 | 3.75 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 63 | 3.48 | 136.59 | H-Bond (Ligand Donor) |
| O5' | OE2 | GLU- 63 | 2.6 | 167.09 | H-Bond (Ligand Donor) |
| N3 | O | VAL- 90 | 3.01 | 168.61 | H-Bond (Ligand Donor) |
| C6 | CB | HIS- 98 | 4.44 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 122 | 3.58 | 0 | Hydrophobic |
| O4' | O | PHE- 123 | 3.19 | 158.57 | H-Bond (Ligand Donor) |
| C5' | CB | PHE- 123 | 4.33 | 0 | Hydrophobic |
| O5' | N | PHE- 123 | 2.91 | 147.39 | H-Bond (Protein Donor) |
| O2 | O | HOH- 313 | 2.87 | 142.81 | H-Bond (Protein Donor) |
