sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.260 Å
X-ray
2009-08-06
| Name: | Redox-sensing transcriptional repressor Rex |
|---|---|
| ID: | REX_THET2 |
| AC: | Q72I39 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 262724 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 75 % |
| B | 25 % |
| B-Factor: | 35.953 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.082 | 469.125 |
| % Hydrophobic | % Polar |
|---|---|
| 54.68 | 45.32 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.07 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -8.29025 | -3.60125 | -15.1924 |
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 | ARG- 90 | 3.33 | 160.51 | H-Bond (Protein Donor) |
| O2N | N | LEU- 91 | 3.1 | 168.88 | H-Bond (Protein Donor) |
| C3N | CB | LEU- 91 | 4.33 | 0 | Hydrophobic |
| C5N | CD2 | LEU- 91 | 4.02 | 0 | Hydrophobic |
| C4N | CD2 | LEU- 95 | 3.67 | 0 | Hydrophobic |
| C2D | CE1 | TYR- 98 | 3.68 | 0 | Hydrophobic |
| O2D | OH | TYR- 98 | 3.04 | 123.98 | H-Bond (Protein Donor) |
| O2D | OH | TYR- 98 | 3.04 | 121.78 | H-Bond (Ligand Donor) |
| O3B | OD1 | ASP- 112 | 2.76 | 136.17 | H-Bond (Ligand Donor) |
| O2B | OD2 | ASP- 112 | 3.12 | 161.27 | H-Bond (Ligand Donor) |
| O3B | NZ | LYS- 117 | 2.82 | 151.17 | H-Bond (Protein Donor) |
| C1B | CG1 | VAL- 148 | 4.34 | 0 | Hydrophobic |
| O3D | O | VAL- 148 | 3.19 | 152.72 | H-Bond (Ligand Donor) |
| C5B | CG | PRO- 149 | 3.87 | 0 | Hydrophobic |
| O2N | O | HOH- 213 | 2.82 | 179.95 | H-Bond (Protein Donor) |
