sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.080 Å
X-ray
2015-07-13
| Name: | Riboflavin biosynthesis protein RibF |
|---|---|
| ID: | RIBF_CORAM |
| AC: | Q59263 |
| Organism: | Corynebacterium ammoniagenes |
| Reign: | Bacteria |
| TaxID: | 1697 |
| EC Number: | 2.7.1.26 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 97 % |
| D | 3 % |
| B-Factor: | 46.968 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.487 | 661.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.31 | 59.69 |
| According to VolSite | |
| HET Code: | ADP |
|---|---|
| Formula: | C10H12N5O10P2 |
| Molecular weight: | 424.177 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.74 % |
| Polar Surface area: | 260.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -42.4197 | 27.5193 | -18.143 |
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 |
| C3' | CG1 | VAL- 193 | 4.45 | 0 | Hydrophobic |
| O1B | N | GLY- 196 | 3.42 | 122.68 | H-Bond (Protein Donor) |
| O2B | N | GLY- 196 | 3.06 | 171.33 | H-Bond (Protein Donor) |
| O1B | N | GLY- 198 | 2.66 | 131.33 | H-Bond (Protein Donor) |
| O2A | N | LYS- 202 | 2.95 | 172.64 | H-Bond (Protein Donor) |
| C5' | CB | PRO- 207 | 4.01 | 0 | Hydrophobic |
| O1A | N | THR- 208 | 3.09 | 174.3 | H-Bond (Protein Donor) |
| C3' | CB | ALA- 209 | 4.34 | 0 | Hydrophobic |
| N6 | O | VAL- 271 | 2.88 | 161.7 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 271 | 3 | 168.76 | H-Bond (Protein Donor) |
| N6 | O | ARG- 274 | 2.94 | 143.56 | H-Bond (Ligand Donor) |
| C2' | CB | LEU- 278 | 3.86 | 0 | Hydrophobic |
| O2' | N | LEU- 278 | 2.84 | 159.92 | H-Bond (Protein Donor) |
| O2B | OH | TYR- 279 | 2.55 | 164.2 | H-Bond (Protein Donor) |
| C4' | CZ | TYR- 279 | 3.85 | 0 | Hydrophobic |
| O3B | CA | CA- 1340 | 2.27 | 0 | Metal Acceptor |
| O1A | CA | CA- 1340 | 2.45 | 0 | Metal Acceptor |
