sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.330 Å
X-ray
2012-07-31
| Name: | Lysine-specific demethylase 4A |
|---|---|
| ID: | KDM4A_HUMAN |
| AC: | O75164 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.14.11 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.725 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.342 | 786.375 |
| % Hydrophobic | % Polar |
|---|---|
| 31.76 | 68.24 |
| According to VolSite | |
| HET Code: | 0WS |
|---|---|
| Formula: | C9H6N3O2 |
| Molecular weight: | 188.163 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.04 % |
| Polar Surface area: | 81.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -26.5144 | -20.8469 | -22.6173 |
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 |
| O | OH | TYR- 132 | 2.94 | 134.19 | H-Bond (Protein Donor) |
| O1 | OH | TYR- 132 | 2.66 | 149.56 | H-Bond (Protein Donor) |
| C5 | CD1 | PHE- 185 | 3.4 | 0 | Hydrophobic |
| C1 | CB | PHE- 185 | 3.9 | 0 | Hydrophobic |
| O | NZ | LYS- 206 | 2.97 | 168 | H-Bond (Protein Donor) |
| O | NZ | LYS- 206 | 2.97 | 0 | Ionic (Protein Cationic) |
