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
2010-02-25
| Name: | FAD-dependent pyridine nucleotide-disulfide oxidoreductase |
|---|---|
| ID: | Q2GBV9_NOVAD |
| AC: | Q2GBV9 |
| Organism: | Novosphingobium aromaticivorans |
| Reign: | Bacteria |
| TaxID: | 279238 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.911 |
|---|---|
| Number of residues: | 57 |
| Including | |
| Standard Amino Acids: | 53 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.058 | 1447.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.96 | 58.04 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 75 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -4.90053 | -34.6514 | 0.197547 |
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 |
| O2A | N | HIS- 19 | 3.12 | 162.75 | H-Bond (Protein Donor) |
| C4' | CB | HIS- 19 | 4.28 | 0 | Hydrophobic |
| O2P | N | GLY- 20 | 2.8 | 149.69 | H-Bond (Protein Donor) |
| O2B | NE | ARG- 42 | 2.93 | 135.98 | H-Bond (Protein Donor) |
| N3A | N | ARG- 42 | 3.45 | 145.29 | H-Bond (Protein Donor) |
| C1B | CG | ARG- 42 | 3.86 | 0 | Hydrophobic |
| O2B | OE1 | GLU- 43 | 2.96 | 161.6 | H-Bond (Ligand Donor) |
| O3B | NH2 | ARG- 50 | 2.91 | 147.48 | H-Bond (Protein Donor) |
| C9 | CB | ARG- 50 | 4.4 | 0 | Hydrophobic |
| C7M | CB | LEU- 53 | 4.12 | 0 | Hydrophobic |
| C6 | CB | SER- 54 | 4.4 | 0 | Hydrophobic |
| C7M | CB | SER- 54 | 3.78 | 0 | Hydrophobic |
| O4 | NZ | LYS- 55 | 2.8 | 146.12 | H-Bond (Protein Donor) |
| N5 | NZ | LYS- 55 | 3.27 | 138.17 | H-Bond (Protein Donor) |
| N6A | O | VAL- 88 | 3.12 | 170.18 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 88 | 3.15 | 149.68 | H-Bond (Protein Donor) |
| C7M | CG2 | VAL- 135 | 4.23 | 0 | Hydrophobic |
| C8M | CG | ARG- 136 | 4.23 | 0 | Hydrophobic |
| C6 | CG1 | ILE- 163 | 4.15 | 0 | Hydrophobic |
| C7M | CG2 | ILE- 163 | 3.77 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 163 | 3.71 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 285 | 2.75 | 173.16 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 285 | 4.31 | 0 | Hydrophobic |
| O1P | N | ASP- 285 | 2.85 | 148.63 | H-Bond (Protein Donor) |
| O2 | N | VAL- 304 | 3.08 | 164.52 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 304 | 4.04 | 0 | Hydrophobic |
| C5' | CB | ALA- 307 | 4.05 | 0 | Hydrophobic |
| O1P | O | HOH- 450 | 2.64 | 154.42 | H-Bond (Protein Donor) |
| O2P | O | HOH- 454 | 2.59 | 179.99 | H-Bond (Protein Donor) |
| O2 | O | HOH- 478 | 2.78 | 156.54 | H-Bond (Protein Donor) |
