sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2009-02-26
| Name: | Iodotyrosine deiodinase 1 |
|---|---|
| ID: | IYD1_MOUSE |
| AC: | Q9DCX8 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 1.21.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 64 % |
| B | 36 % |
| B-Factor: | 32.188 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.245 | 459.000 |
| % Hydrophobic | % Polar |
|---|---|
| 29.41 | 70.59 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 81.94 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -40.9088 | 28.4686 | 0.944097 |
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 |
| O4' | O | HOH- 17 | 2.85 | 166.4 | H-Bond (Ligand Donor) |
| O2P | CZ | ARG- 96 | 3.46 | 0 | Ionic (Protein Cationic) |
| O2P | NH2 | ARG- 96 | 3.03 | 145.7 | H-Bond (Protein Donor) |
| O2P | NH1 | ARG- 96 | 3.04 | 144.78 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 96 | 3.06 | 140.55 | H-Bond (Protein Donor) |
| O1P | NE | ARG- 97 | 2.72 | 167.98 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 97 | 3.64 | 0 | Ionic (Protein Cationic) |
| C1' | CB | SER- 98 | 4.34 | 0 | Hydrophobic |
| C3' | CB | SER- 98 | 4.22 | 0 | Hydrophobic |
| O1P | N | SER- 98 | 2.78 | 160.51 | H-Bond (Protein Donor) |
| O2P | N | SER- 98 | 3.39 | 132.73 | H-Bond (Protein Donor) |
| O2P | OG | SER- 98 | 2.62 | 173.13 | H-Bond (Protein Donor) |
| N1 | NH2 | ARG- 100 | 2.9 | 169.1 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 100 | 3.24 | 126.5 | H-Bond (Protein Donor) |
| O2 | NE | ARG- 100 | 2.58 | 161.35 | H-Bond (Protein Donor) |
| C8M | CB | PRO- 123 | 4.04 | 0 | Hydrophobic |
| C9 | CB | PRO- 123 | 4.38 | 0 | Hydrophobic |
| O3' | N | SER- 124 | 3.27 | 138 | H-Bond (Protein Donor) |
| C4' | CB | HIS- 127 | 3.92 | 0 | Hydrophobic |
| C7M | CB | TYR- 208 | 3.7 | 0 | Hydrophobic |
| C7M | CG2 | ILE- 211 | 3.99 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 215 | 4.07 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 232 | 4.1 | 0 | Hydrophobic |
| C8M | CG2 | THR- 233 | 4.04 | 0 | Hydrophobic |
| C9 | CB | THR- 233 | 4.13 | 0 | Hydrophobic |
| O4 | N | THR- 235 | 3.03 | 176.46 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 235 | 3.09 | 152.35 | H-Bond (Protein Donor) |
| C7M | CG2 | THR- 235 | 4.2 | 0 | Hydrophobic |
| C6 | CG2 | THR- 235 | 3.59 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 273 | 3.82 | 0 | Hydrophobic |
| O3P | NH2 | ARG- 275 | 2.77 | 152.52 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 275 | 3.75 | 0 | Ionic (Protein Cationic) |
| N3 | O | IYR- 302 | 2.78 | 160.78 | H-Bond (Ligand Donor) |
| O4 | N | IYR- 302 | 2.81 | 154.37 | H-Bond (Protein Donor) |
| O2' | OF | IYR- 302 | 2.54 | 149.91 | H-Bond (Protein Donor) |
| C6 | IE | IYR- 302 | 4.32 | 0 | Hydrophobic |
| O3P | O | HOH- 553 | 2.76 | 179.95 | H-Bond (Protein Donor) |
