Research workbench
LSD1-COREST1 in complex with quinazoline-derivative reversible inhibitor
Analyse LSD1-COREST1 in complex with quinazoline-derivative reversible inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L3E
- 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
- E11, FAD, NA
- Pockets
- 7 · best druggability 0.83
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 | 666 | 45% helix, 15% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 65% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- E11 · N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino) propyl]-6,7-dimethoxyquinazoline-2,4-diamine · ligand · 5 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.83 | 0.84 | 90 | FAD, E11, NA |
| 2 | 335 | 0.62 | 0.79 | 28 | empty |
| 3 | 203 | 0.48 | 0.75 | 25 | empty |
| 4 | 167 | 0.45 | 0.75 | 30 | empty |
| 5 | 88 | 0.43 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2765 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5L3E · LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor · 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 0.94
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 5L3E · PDBe 5L3E · UniProt O60341 · UniProt Q9UKL0
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