sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2008-11-13
| Name: | Flavodoxin |
|---|---|
| ID: | FLAV_DESDE |
| AC: | P26492 |
| Organism: | Desulfovibrio desulfuricans |
| Reign: | Bacteria |
| TaxID: | 876 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 19 % |
| E | 81 % |
| B-Factor: | 39.895 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.239 | 1029.375 |
| % Hydrophobic | % Polar |
|---|---|
| 50.16 | 49.84 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 71.45 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -41.6055 | -38.8802 | -5.78703 |
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 |
| O1P | OG | SER- 10 | 3.3 | 123.98 | H-Bond (Protein Donor) |
| O3P | OG | SER- 10 | 2.82 | 162.87 | H-Bond (Protein Donor) |
| O2P | N | SER- 11 | 3.22 | 158.11 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 12 | 2.6 | 162.73 | H-Bond (Protein Donor) |
| O1P | N | THR- 12 | 2.91 | 132 | H-Bond (Protein Donor) |
| O2P | N | THR- 12 | 3.48 | 160.93 | H-Bond (Protein Donor) |
| C5' | CB | ASN- 14 | 3.91 | 0 | Hydrophobic |
| O1P | ND2 | ASN- 14 | 3.35 | 149.52 | H-Bond (Protein Donor) |
| O1P | N | ASN- 14 | 2.76 | 152.67 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 15 | 2.77 | 137.89 | H-Bond (Protein Donor) |
| O3P | N | THR- 15 | 2.89 | 159.38 | H-Bond (Protein Donor) |
| C4' | CB | SER- 58 | 4.06 | 0 | Hydrophobic |
| O2' | O | ALA- 59 | 2.52 | 168.4 | H-Bond (Ligand Donor) |
| C7M | CE3 | TRP- 60 | 4.11 | 0 | Hydrophobic |
| C4' | CZ2 | TRP- 60 | 4.25 | 0 | Hydrophobic |
| C8 | CZ3 | TRP- 60 | 3.36 | 0 | Hydrophobic |
| N5 | N | GLY- 61 | 3.18 | 172.52 | H-Bond (Protein Donor) |
| C5' | CB | SER- 93 | 4.38 | 0 | Hydrophobic |
| N1 | N | ASP- 95 | 3.26 | 139.63 | H-Bond (Protein Donor) |
| O2 | N | ASP- 95 | 3.23 | 156.28 | H-Bond (Protein Donor) |
| C1' | CB | ASP- 95 | 3.9 | 0 | Hydrophobic |
| C1' | CE1 | TYR- 98 | 3.84 | 0 | Hydrophobic |
| N3 | O | HIS- 100 | 2.77 | 171.06 | H-Bond (Ligand Donor) |
| O2 | N | CYS- 102 | 3.22 | 153.34 | H-Bond (Protein Donor) |
| C7M | CB | ALA- 138 | 3.72 | 0 | Hydrophobic |
| C8M | CB | SER- 139 | 4.03 | 0 | Hydrophobic |
| C8M | CB | GLU- 142 | 4.34 | 0 | Hydrophobic |
