sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2013-12-17
| Name: | Probable Histone-lysine N-methyltransferase ATXR5 |
|---|---|
| ID: | ATXR5_RICCO |
| AC: | B9RU15 |
| Organism: | Ricinus communis |
| Reign: | Eukaryota |
| TaxID: | 3988 |
| EC Number: | 2.1.1.43 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 37.713 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.237 | 1127.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.22 | 60.78 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 68.77 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -33.8362 | -7.48831 | -0.978346 |
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 |
| N | O | PHE- 252 | 2.96 | 171.07 | H-Bond (Ligand Donor) |
| OXT | N | PHE- 252 | 2.83 | 150.83 | H-Bond (Protein Donor) |
| SD | CB | SER- 286 | 4.24 | 0 | Hydrophobic |
| O | NH2 | ARG- 312 | 3.05 | 139.24 | H-Bond (Protein Donor) |
| CB | CD1 | PHE- 313 | 4.36 | 0 | Hydrophobic |
| N7 | N | GLY- 316 | 3.08 | 173.17 | H-Bond (Protein Donor) |
| N6 | O | GLY- 316 | 2.85 | 151.32 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 361 | 3.83 | 0 | Hydrophobic |
| C5' | CZ | TYR- 368 | 4.3 | 0 | Hydrophobic |
| C3' | CZ | TYR- 368 | 4.19 | 0 | Hydrophobic |
| O3' | OH | TYR- 368 | 2.59 | 160.01 | H-Bond (Ligand Donor) |
| C3' | CZ | PHE- 373 | 3.84 | 0 | Hydrophobic |
| C2' | CE2 | PHE- 373 | 3.88 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 373 | 3.93 | 0 | Aromatic Face/Face |
| N6 | O | VAL- 374 | 3.14 | 174.47 | H-Bond (Ligand Donor) |
| N1 | N | VAL- 374 | 2.76 | 166.48 | H-Bond (Protein Donor) |
