sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-06-14
| Name: | Rubredoxin-NAD(+) reductase |
|---|---|
| ID: | RURE_PSEAE |
| AC: | Q9HTK9 |
| Organism: | Pseudomonas aeruginosa |
| Reign: | Bacteria |
| TaxID: | 208964 |
| EC Number: | 1.18.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.722 |
|---|---|
| Number of residues: | 57 |
| Including | |
| Standard Amino Acids: | 53 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.088 | 658.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.03 | 58.97 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 67.8 % |
| 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 |
|---|---|---|
| 86.4436 | 31.0138 | 16.6458 |
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 |
| O3B | N | THR- 12 | 3.05 | 153.69 | H-Bond (Protein Donor) |
| C4' | CD1 | LEU- 14 | 4.43 | 0 | Hydrophobic |
| O1P | N | ALA- 15 | 3.02 | 162.66 | H-Bond (Protein Donor) |
| O3B | OG1 | THR- 36 | 3.1 | 159.04 | H-Bond (Protein Donor) |
| O2B | N | ALA- 37 | 3.37 | 129.28 | H-Bond (Protein Donor) |
| N3A | N | ALA- 37 | 3.1 | 123.51 | H-Bond (Protein Donor) |
| O2B | N | ASP- 38 | 3.41 | 137.08 | H-Bond (Protein Donor) |
| O1A | NZ | LYS- 45 | 2.69 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 45 | 3.03 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 45 | 3.03 | 145.81 | H-Bond (Protein Donor) |
| C8 | CG | LYS- 45 | 4.32 | 0 | Hydrophobic |
| C8M | CD | LYS- 45 | 3.77 | 0 | Hydrophobic |
| C9 | CD | LYS- 45 | 4.25 | 0 | Hydrophobic |
| C2' | CG | PRO- 46 | 4.49 | 0 | Hydrophobic |
| C7M | CB | LEU- 48 | 4.28 | 0 | Hydrophobic |
| C6 | CB | SER- 49 | 4.49 | 0 | Hydrophobic |
| C7M | CB | SER- 49 | 3.99 | 0 | Hydrophobic |
| N6A | O | VAL- 83 | 3.11 | 166.96 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 83 | 2.88 | 166.1 | H-Bond (Protein Donor) |
| C7M | CG2 | ILE- 156 | 4.15 | 0 | Hydrophobic |
| C7 | CG1 | ILE- 156 | 3.74 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 156 | 3.59 | 0 | Hydrophobic |
| C7M | CZ | PHE- 160 | 3.63 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 277 | 2.56 | 168.63 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 277 | 4.27 | 0 | Hydrophobic |
| O2P | N | ASP- 277 | 3.11 | 155.35 | H-Bond (Protein Donor) |
| O2 | N | VAL- 289 | 2.84 | 160.13 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 289 | 4.07 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 292 | 3.95 | 0 | Hydrophobic |
| O4 | NZ | LYS- 320 | 2.93 | 173.04 | H-Bond (Protein Donor) |
| O2P | O | HOH- 2156 | 2.85 | 179.96 | H-Bond (Protein Donor) |
| O1P | O | HOH- 2228 | 2.6 | 179.98 | H-Bond (Protein Donor) |
| O1A | O | HOH- 2229 | 2.69 | 179.99 | H-Bond (Protein Donor) |
| O3B | O | HOH- 2231 | 2.64 | 167.76 | H-Bond (Ligand Donor) |
