sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2002-12-02
| Name: | Riboflavin kinase |
|---|---|
| ID: | RIFK_HUMAN |
| AC: | Q969G6 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.1.26 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.570 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ADP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.347 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.78 | 47.22 |
| According to VolSite | |
| HET Code: | RBF |
|---|---|
| Formula: | C17H20N4O6 |
| Molecular weight: | 376.364 g/mol |
| DrugBank ID: | DB00140 |
| Buried Surface Area: | 49.62 % |
| 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 |
|---|---|---|
| 0.413667 | 32.1407 | 33.7523 |
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 |
| C4' | CB | SER- 27 | 4.21 | 0 | Hydrophobic |
| C8M | CG2 | THR- 34 | 3.85 | 0 | Hydrophobic |
| C7M | CG2 | ILE- 53 | 3.8 | 0 | Hydrophobic |
| C9A | CD1 | ILE- 53 | 4.5 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 53 | 3.37 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 69 | 3.56 | 0 | Hydrophobic |
| C9 | CB | SER- 71 | 3.86 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 86 | 2.6 | 154.91 | H-Bond (Ligand Donor) |
| O5' | OE1 | GLU- 86 | 2.83 | 139.82 | H-Bond (Ligand Donor) |
| O4 | NH1 | ARG- 111 | 2.78 | 165.05 | H-Bond (Protein Donor) |
| O4 | NH2 | ARG- 111 | 3.29 | 134.16 | H-Bond (Protein Donor) |
| N5 | NH2 | ARG- 111 | 3.04 | 131.29 | H-Bond (Protein Donor) |
| N3 | O | LYS- 114 | 2.8 | 170 | H-Bond (Ligand Donor) |
| O4 | N | LYS- 114 | 3.03 | 150.22 | H-Bond (Protein Donor) |
| C7M | CG2 | ILE- 126 | 4.03 | 0 | Hydrophobic |
| C8M | CG2 | ILE- 126 | 4.15 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 126 | 4.01 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 126 | 3.87 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 126 | 3.84 | 0 | Hydrophobic |
| C7M | CB | ASP- 129 | 4.17 | 0 | Hydrophobic |
