Research workbench
LSD1-corest in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(P-tolyl) pyridin-3-YL]BENZONITRILE
Analyse LSD1-corest in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(P-tolyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YJB
- Type
- protein
- Length
- 792 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
- FAD, 8WC
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 661 | 46% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 131 | 64% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 8WC · 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.82 | 0.83 | 94 | FAD, 8WC |
| 2 | 348 | 0.63 | 0.78 | 29 | empty |
| 3 | 169 | 0.48 | 0.77 | 26 | empty |
| 4 | 78 | 0.44 | 0.80 | 18 | empty |
| 5 | 100 | 0.40 | 0.76 | 21 | GOL |
Interfaces
1 interface between chains.
- A–B · 2716 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5YJB · LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitr… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UKL0 · AlphaFold monomer V2.0 prediction for rest corepressor 1 (Q9UKL0) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 5YJB · PDBe 5YJB · UniProt O60341 · UniProt Q9UKL0
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