sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2004-09-16
| Name: | Ferredoxin--NADP reductase |
|---|---|
| ID: | FENR_NOSSO |
| AC: | P21890 |
| Organism: | Nostoc sp. |
| Reign: | Bacteria |
| TaxID: | 1168 |
| EC Number: | 1.18.1.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 86 % |
| B | 14 % |
| B-Factor: | 28.985 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | NAP FAD |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.406 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 46.51 | 53.49 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 54.9 % |
| 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 |
|---|---|---|
| 153.365 | 69.6694 | -7.71315 |
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 |
| O1A | NH2 | ARG- 77 | 3.23 | 137.34 | H-Bond (Protein Donor) |
| O1P | NH2 | ARG- 77 | 3.16 | 134.35 | H-Bond (Protein Donor) |
| O1P | NE | ARG- 77 | 2.99 | 142.96 | H-Bond (Protein Donor) |
| C2' | CB | ARG- 77 | 4.25 | 0 | Hydrophobic |
| C3' | CG | ARG- 77 | 4.06 | 0 | Hydrophobic |
| O1P | CZ | ARG- 77 | 3.48 | 0 | Ionic (Protein Cationic) |
| C7M | CD1 | LEU- 78 | 4.09 | 0 | Hydrophobic |
| C8 | CB | LEU- 78 | 3.82 | 0 | Hydrophobic |
| O2' | O | LEU- 78 | 3.2 | 137.39 | H-Bond (Ligand Donor) |
| C3' | CZ | TYR- 79 | 4.44 | 0 | Hydrophobic |
| C4' | CE1 | TYR- 79 | 4.22 | 0 | Hydrophobic |
| C2' | CE1 | TYR- 79 | 3.86 | 0 | Hydrophobic |
| O4' | OH | TYR- 79 | 2.76 | 151.89 | H-Bond (Ligand Donor) |
| O4 | N | SER- 80 | 3.42 | 141.9 | H-Bond (Protein Donor) |
| N5 | N | SER- 80 | 3.34 | 147.17 | H-Bond (Protein Donor) |
| N5 | OG | SER- 80 | 3.4 | 162.76 | H-Bond (Protein Donor) |
| N3 | O | CYS- 98 | 3.17 | 147.78 | H-Bond (Ligand Donor) |
| O2 | N | ARG- 100 | 3.42 | 146.5 | H-Bond (Protein Donor) |
| C5B | CD2 | LEU- 102 | 4.25 | 0 | Hydrophobic |
| C5' | CD2 | LEU- 102 | 4.31 | 0 | Hydrophobic |
| C1B | CZ | TYR- 104 | 4.1 | 0 | Hydrophobic |
| DuAr | DuAr | TYR- 104 | 3.56 | 0 | Aromatic Face/Face |
| O2A | N | VAL- 116 | 2.76 | 154.97 | H-Bond (Protein Donor) |
| O1P | N | CYS- 117 | 2.74 | 134.72 | H-Bond (Protein Donor) |
| C5' | CB | SER- 118 | 4.05 | 0 | Hydrophobic |
| O2P | N | SER- 118 | 3.15 | 157.5 | H-Bond (Protein Donor) |
| C9 | CB | TRP- 303 | 3.77 | 0 | Hydrophobic |
