sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2011-05-06
| 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: | 31.709 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.659 | 837.000 |
| % Hydrophobic | % Polar |
|---|---|
| 36.69 | 63.31 |
| According to VolSite | |
| HET Code: | HQ2 |
|---|---|
| Formula: | C14H15N3O3 |
| Molecular weight: | 273.287 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.92 % |
| Polar Surface area: | 93.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -25.0155 | -20.4409 | -21.9384 |
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 |
| CAN | CE2 | TYR- 132 | 4.31 | 0 | Hydrophobic |
| OAS | OH | TYR- 132 | 3 | 126.43 | H-Bond (Protein Donor) |
| OAT | OH | TYR- 132 | 2.52 | 162.08 | H-Bond (Protein Donor) |
| CAN | CB | ALA- 134 | 4.11 | 0 | Hydrophobic |
| NAC | OD1 | ASP- 135 | 3.11 | 156.44 | H-Bond (Ligand Donor) |
| NAC | OD2 | ASP- 135 | 3.02 | 127.78 | H-Bond (Ligand Donor) |
| NAC | OD1 | ASP- 135 | 3.11 | 0 | Ionic (Ligand Cationic) |
| NAC | OD2 | ASP- 135 | 3.02 | 0 | Ionic (Ligand Cationic) |
| CAN | CE2 | TYR- 177 | 3.48 | 0 | Hydrophobic |
| CAQ | CE2 | TYR- 177 | 4.08 | 0 | Hydrophobic |
| CAG | CB | PHE- 185 | 3.66 | 0 | Hydrophobic |
| CAF | CG | PHE- 185 | 3.41 | 0 | Hydrophobic |
| OAS | NZ | LYS- 206 | 2.64 | 173.32 | H-Bond (Protein Donor) |
| OAS | NZ | LYS- 206 | 2.64 | 0 | Ionic (Protein Cationic) |
| CAD | CH2 | TRP- 208 | 3.37 | 0 | Hydrophobic |
| OAR | NE2 | HIS- 276 | 2.53 | 158.06 | H-Bond (Protein Donor) |
