MolNFT v1 · #165423 · protein
Human LSD1/COREST bound to the quinazoline inhibitor MC4106
6TUY · Lysine-specific histone demethylase 1A: “Human LSD1/COREST bound to the quinazoline inhibitor MC4106”. X-ray diffraction, 4 ligands (NY8, FAD, CL), 8 pockets (best druggability 0.82). MolNFT v1 #165423 on GenesisL1: 3D structure…
- PDB
- 6TUY
- Type
- protein
- Length
- 801 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
- NY8, FAD, CL, PO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 667 | 45% helix, 15% strand | O60341 |
| B | Rest corepressor 1 | protein | 134 | 65% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- NY8 · ~{N}2-[3-(dimethylamino)propyl]-6,7-dimethoxy-~{N}4-[1-(naphthalen-2-ylmethyl)piperidin-4-yl]quinazoline-2,4-diamine · ligand · 3 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- CL · Chloride ion · ion · 5 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.82 | 0.83 | 92 | FAD, NY8 |
| 2 | 395 | 0.63 | 0.78 | 36 | empty |
| 3 | 284 | 0.56 | 0.76 | 32 | empty |
| 4 | 66 | 0.53 | 0.87 | 24 | empty |
| 5 | 101 | 0.43 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2805 Ų buried · 24 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 6TUY · PDBe 6TUY · UniProt O60341 · UniProt Q9UKL0
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