sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2013-06-25
| Name: | Ketimine reductase mu-crystallin |
|---|---|
| ID: | CRYM_MOUSE |
| AC: | O54983 |
| Organism: | Mus musculus |
| Reign: | Eukaryota |
| TaxID: | 10090 |
| EC Number: | 1.5.1.25 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 17.615 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.104 | 607.500 |
| % Hydrophobic | % Polar |
|---|---|
| 58.33 | 41.67 |
| According to VolSite | |
| HET Code: | T3 |
|---|---|
| Formula: | C15H12I3NO4 |
| Molecular weight: | 650.973 g/mol |
| DrugBank ID: | DB00279 |
| Buried Surface Area: | 68.49 % |
| Polar Surface area: | 97.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 23.9777 | -6.23709 | 11.223 |
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 |
| I2 | CD | ARG- 47 | 4.14 | 0 | Hydrophobic |
| O4 | CZ | ARG- 47 | 3.21 | 0 | Ionic (Protein Cationic) |
| I2 | CG2 | VAL- 49 | 4.12 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 49 | 3.9 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 49 | 3.97 | 0 | Hydrophobic |
| I3 | CB | PHE- 58 | 4.07 | 0 | Hydrophobic |
| C12 | CG | PHE- 58 | 3.42 | 0 | Hydrophobic |
| C12 | CB | PHE- 58 | 3.91 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 77 | 4.17 | 0 | Hydrophobic |
| I3 | CG1 | VAL- 77 | 4.29 | 0 | Hydrophobic |
| I1 | CD2 | PHE- 79 | 3.68 | 0 | Hydrophobic |
| I3 | CB | PHE- 79 | 4.44 | 0 | Hydrophobic |
| C7 | CB | PHE- 79 | 3.45 | 0 | Hydrophobic |
| I1 | CD | ARG- 229 | 3.73 | 0 | Hydrophobic |
| C8 | CG | ARG- 229 | 3.5 | 0 | Hydrophobic |
| I1 | CZ3 | TRP- 232 | 3.61 | 0 | Hydrophobic |
| I2 | CG | GLU- 256 | 3.72 | 0 | Hydrophobic |
| C13 | C2D | NDP- 1313 | 4.29 | 0 | Hydrophobic |
| N1 | O2D | NDP- 1313 | 2.97 | 160.42 | H-Bond (Ligand Donor) |
| O4 | O | HOH- 2076 | 2.83 | 149.79 | H-Bond (Protein Donor) |
