sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2004-05-07
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 77.620 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.584 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.64 | 44.36 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 49.79 % |
| 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 |
|---|---|---|
| -16.471 | -3.32681 | 33.8801 |
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- 480 | 3.47 | 0 | Hydrophobic |
| C7M | CG1 | VAL- 497 | 3.72 | 0 | Hydrophobic |
| C7M | CG1 | VAL- 513 | 3.31 | 0 | Hydrophobic |
| C9 | CB | ASN- 515 | 3.78 | 0 | Hydrophobic |
| O4' | OE1 | GLU- 531 | 2.61 | 136.62 | H-Bond (Ligand Donor) |
| O4' | OE2 | GLU- 531 | 2.67 | 137.79 | H-Bond (Ligand Donor) |
| C8M | CB | TYR- 533 | 3.99 | 0 | Hydrophobic |
| N5 | NH2 | ARG- 555 | 3.1 | 134.19 | H-Bond (Protein Donor) |
| N3 | O | LYS- 558 | 2.75 | 157.98 | H-Bond (Ligand Donor) |
| O4 | N | LYS- 558 | 3.01 | 174.02 | H-Bond (Protein Donor) |
| C9A | CD1 | LEU- 566 | 4.29 | 0 | Hydrophobic |
| C2' | CD2 | LEU- 566 | 4.4 | 0 | Hydrophobic |
| C7M | CG2 | ILE- 570 | 4.32 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 570 | 3.84 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 570 | 3.87 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 570 | 3.82 | 0 | Hydrophobic |
| C7M | CB | ASP- 573 | 4.11 | 0 | Hydrophobic |
