Research workbench
Structure of the KDM1A/COREST complex with the inhibitor 2-[3-{4- chloro-3-[(4-CHLOROPHENYL)ETHYNYL]PHENYL}-1-(3-morpholin-4-ylpropyl)- 1,4,6,7-tetrahydro-5H-PYRAZOLO[4,3-C]PYRIDIN-5-yl]-2-oxoethanol
Analyse Structure of the KDM1A/COREST complex with the inhibitor 2-[3-{4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TE1
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- N4K, FAD
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 44% helix, 17% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- N4K · 5-[4-cyclobutyl-1-[2-(4-piperidin-4-yloxyphenoxy) ethyl]imidazol-2-yl]-4-methyl-thieno[3,2-b]pyrrole · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.82 | 0.83 | 93 | N4K, FAD |
| 2 | 346 | 0.60 | 0.77 | 31 | empty |
| 3 | 191 | 0.48 | 0.76 | 26 | empty |
| 4 | 93 | 0.45 | 0.79 | 19 | empty |
| 5 | 148 | 0.41 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2777 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O60341
- Every structure of UniProt Q9UKL0
- Elsewhere: RCSB PDB 6TE1 · PDBe 6TE1 · UniProt O60341 · UniProt Q9UKL0
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