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
2001-06-27
| Name: | Thioredoxin reductase 1, cytoplasmic |
|---|---|
| ID: | TRXR1_RAT |
| AC: | O89049 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | 1.8.1.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 94 % |
| B | 6 % |
| B-Factor: | 12.449 |
|---|---|
| Number of residues: | 65 |
| Including | |
| Standard Amino Acids: | 65 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.129 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 49.05 | 50.95 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 74.23 % |
| 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 |
|---|---|---|
| 25.8692 | 20.544 | 120.153 |
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 | SER- 22 | 2.92 | 169.4 | H-Bond (Protein Donor) |
| C4' | CB | SER- 22 | 4.32 | 0 | Hydrophobic |
| O1P | N | GLY- 23 | 2.83 | 172.86 | H-Bond (Protein Donor) |
| O3B | OD1 | ASP- 42 | 2.74 | 160.19 | H-Bond (Ligand Donor) |
| O2B | O | PHE- 43 | 2.92 | 144.9 | H-Bond (Ligand Donor) |
| N3A | N | PHE- 43 | 3 | 141.79 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 58 | 2.51 | 150.16 | H-Bond (Protein Donor) |
| O1A | N | THR- 58 | 3.4 | 148.54 | H-Bond (Protein Donor) |
| O2A | N | THR- 58 | 3.49 | 142.41 | H-Bond (Protein Donor) |
| C8M | CG2 | THR- 58 | 3.84 | 0 | Hydrophobic |
| C9A | SG | CYS- 64 | 4.22 | 0 | Hydrophobic |
| C2' | SG | CYS- 64 | 4.29 | 0 | Hydrophobic |
| O4 | NZ | LYS- 67 | 3.04 | 127.54 | H-Bond (Protein Donor) |
| N6A | O | GLY- 132 | 3.22 | 153.05 | H-Bond (Ligand Donor) |
| N1A | N | GLY- 132 | 2.78 | 171.57 | H-Bond (Protein Donor) |
| C7M | CB | SER- 180 | 3.76 | 0 | Hydrophobic |
| C7M | CE2 | PHE- 184 | 4.49 | 0 | Hydrophobic |
| C7M | CG2 | VAL- 201 | 3.53 | 0 | Hydrophobic |
| C8M | CD | ARG- 293 | 3.59 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 334 | 2.78 | 169.57 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 334 | 3.15 | 123.12 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 334 | 4.41 | 0 | Hydrophobic |
| O2P | N | ASP- 334 | 3.13 | 159.08 | H-Bond (Protein Donor) |
| C2' | CB | THR- 343 | 4.42 | 0 | Hydrophobic |
| C4' | CB | THR- 343 | 4.35 | 0 | Hydrophobic |
| N3 | O | HIS- 472 | 2.63 | 142.45 | H-Bond (Ligand Donor) |
