sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2008-01-08
| Name: | Putative 2-nitropropane dioxygenase |
|---|---|
| ID: | Q9FDD4_9ACTN |
| AC: | Q9FDD4 |
| Organism: | Streptomyces ansochromogenes |
| Reign: | Bacteria |
| TaxID: | 115647 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 21.546 |
|---|---|
| Number of residues: | 49 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.991 | 813.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.13 | 51.87 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 73 % |
| 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 |
|---|---|---|
| -54.7888 | 19.3003 | -56.2227 |
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 |
| C2' | CB | ALA- 16 | 3.61 | 0 | Hydrophobic |
| C7M | SD | MET- 18 | 3.92 | 0 | Hydrophobic |
| C8M | SD | MET- 18 | 3.99 | 0 | Hydrophobic |
| C7 | CG | MET- 18 | 4.07 | 0 | Hydrophobic |
| O4 | N | ALA- 19 | 3.23 | 135.69 | H-Bond (Protein Donor) |
| C7M | CG2 | VAL- 22 | 4.24 | 0 | Hydrophobic |
| N3 | OD1 | ASN- 68 | 2.92 | 149.82 | H-Bond (Ligand Donor) |
| O3' | NE2 | GLN- 172 | 3.03 | 142.68 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 176 | 3.62 | 0 | Hydrophobic |
| O5' | N | GLY- 177 | 3.14 | 161.61 | H-Bond (Protein Donor) |
| O1P | N | GLY- 177 | 3.31 | 143.24 | H-Bond (Protein Donor) |
| C3' | CB | ALA- 214 | 4.43 | 0 | Hydrophobic |
| C5' | CB | ALA- 214 | 4.3 | 0 | Hydrophobic |
| O3P | N | GLY- 216 | 2.78 | 152.45 | H-Bond (Protein Donor) |
| O2' | OE1 | GLN- 235 | 3.09 | 147.89 | H-Bond (Ligand Donor) |
| O2P | N | GLY- 237 | 3.01 | 175.41 | H-Bond (Protein Donor) |
| O1P | N | THR- 238 | 3.03 | 160.62 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 238 | 2.79 | 149.78 | H-Bond (Protein Donor) |
| C7M | CD2 | LEU- 241 | 3.87 | 0 | Hydrophobic |
| C8M | CD2 | LEU- 241 | 4.44 | 0 | Hydrophobic |
| C8M | CB | TYR- 320 | 4.37 | 0 | Hydrophobic |
| C7 | CB | TYR- 320 | 3.61 | 0 | Hydrophobic |
| O2P | O | HOH- 375 | 2.84 | 166.91 | H-Bond (Protein Donor) |
| O4 | O | HOH- 398 | 2.91 | 179.95 | H-Bond (Protein Donor) |
