sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2004-01-16
| Name: | Riboflavin biosynthesis protein |
|---|---|
| ID: | Q9WZW1_THEMA |
| AC: | Q9WZW1 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 243274 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 51.633 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.496 | 432.000 |
| % Hydrophobic | % Polar |
|---|---|
| 62.50 | 37.50 |
| According to VolSite | |
| HET Code: | LUM |
|---|---|
| Formula: | C12H10N4O2 |
| Molecular weight: | 242.233 g/mol |
| DrugBank ID: | DB04345 |
| Buried Surface Area: | 62.13 % |
| Polar Surface area: | 83.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 36.0531 | -6.21267 | 23.2877 |
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 | CG2 | THR- 180 | 3.77 | 0 | Hydrophobic |
| C7M | CG1 | VAL- 197 | 4.04 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 197 | 3.39 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 213 | 3.38 | 0 | Hydrophobic |
| C8 | CB | ASN- 215 | 3.53 | 0 | Hydrophobic |
| C8M | CB | TYR- 233 | 4.08 | 0 | Hydrophobic |
| O4 | NH1 | ARG- 255 | 2.88 | 176.74 | H-Bond (Protein Donor) |
| N5 | NH2 | ARG- 255 | 3.08 | 139.72 | H-Bond (Protein Donor) |
| N3 | O | LYS- 258 | 2.51 | 157.48 | H-Bond (Ligand Donor) |
| O4 | N | LYS- 258 | 2.61 | 141.74 | H-Bond (Protein Donor) |
| C9A | CD1 | LEU- 266 | 4.37 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 270 | 3.86 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 270 | 3.71 | 0 | Hydrophobic |
| C7M | CB | ASP- 273 | 4.23 | 0 | Hydrophobic |
