sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2016-04-06
| Name: | Lysine-specific histone demethylase 1A |
|---|---|
| ID: | KDM1A_HUMAN |
| AC: | O60341 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 56.392 |
|---|---|
| Number of residues: | 63 |
| Including | |
| Standard Amino Acids: | 63 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.284 | 894.375 |
| % Hydrophobic | % Polar |
|---|---|
| 53.96 | 46.04 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 79.18 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| -6.84725 | 65.3416 | 86.8437 |
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 |
| O1P | N | SER- 289 | 3.11 | 158.08 | H-Bond (Protein Donor) |
| O1P | OG | SER- 289 | 2.59 | 161.38 | H-Bond (Protein Donor) |
| O3B | OE2 | GLU- 308 | 3.12 | 123.11 | H-Bond (Ligand Donor) |
| O3B | OE1 | GLU- 308 | 2.51 | 155.28 | H-Bond (Ligand Donor) |
| O2B | OE2 | GLU- 308 | 2.65 | 170.15 | H-Bond (Ligand Donor) |
| N3A | N | ALA- 309 | 3.32 | 145.64 | H-Bond (Protein Donor) |
| O1A | NE | ARG- 316 | 2.91 | 178.33 | H-Bond (Protein Donor) |
| O2A | N | ARG- 316 | 3.13 | 169.23 | H-Bond (Protein Donor) |
| O3P | NH2 | ARG- 316 | 3.18 | 131.65 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 316 | 3.71 | 0 | Ionic (Protein Cationic) |
| C8M | CG | ARG- 316 | 4.46 | 0 | Hydrophobic |
| C3' | CB | ARG- 316 | 4.13 | 0 | Hydrophobic |
| C9A | CB | ALA- 331 | 4.16 | 0 | Hydrophobic |
| C2' | CB | ALA- 331 | 4.07 | 0 | Hydrophobic |
| N3 | O | VAL- 333 | 3.03 | 143.54 | H-Bond (Ligand Donor) |
| O4 | N | VAL- 333 | 3.2 | 134.35 | H-Bond (Protein Donor) |
| N6A | O | VAL- 590 | 3.09 | 163.89 | H-Bond (Ligand Donor) |
| N1A | N | VAL- 590 | 3.02 | 151.27 | H-Bond (Protein Donor) |
| C5B | CG | PRO- 626 | 4.06 | 0 | Hydrophobic |
| C7M | CG | LEU- 659 | 4.24 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 659 | 4.31 | 0 | Hydrophobic |
| C7M | CG | LYS- 661 | 4.39 | 0 | Hydrophobic |
| C8M | CE2 | TRP- 751 | 3.87 | 0 | Hydrophobic |
| C2B | CB | TRP- 756 | 3.92 | 0 | Hydrophobic |
| C8M | CB | SER- 760 | 3.21 | 0 | Hydrophobic |
| C3' | CG | GLU- 801 | 4.35 | 0 | Hydrophobic |
| C5' | CB | GLU- 801 | 3.96 | 0 | Hydrophobic |
| O2P | N | GLU- 801 | 2.87 | 142.1 | H-Bond (Protein Donor) |
| O3' | O | THR- 810 | 3.41 | 121.91 | H-Bond (Ligand Donor) |
| O2 | N | VAL- 811 | 3.07 | 169.75 | H-Bond (Protein Donor) |
| C2' | CG2 | VAL- 811 | 3.88 | 0 | Hydrophobic |
| C5' | CB | ALA- 814 | 4.25 | 0 | Hydrophobic |
