MolNFT v1 · #125723 · protein
Structure of the KDM1A/COREST complex with the inhibitor N-[3- (ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3- YL]METHOXY]PHENOXY]METHYL]PHENYL]-4-METHYLTHIENO[3,2-B]PYRROLE-5- carboxamide
5LHI · Lysine-specific histone demethylase 1: “Structure of the KDM1A/COREST complex with the inhibitor N-[3- (ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3…”. X-ray diffraction, 2 ligands (FAD, 6X5), 8 pockets (best druggability 0.82). MolNFT…
- PDB
- 5LHI
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1; Rest corepressor 1
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD, 6X5
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1 | protein | 666 | 42% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 50% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 6X5 · ~{N}-[3-(ethoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.82 | 0.83 | 94 | FAD, 6X5 |
| 2 | 379 | 0.62 | 0.77 | 32 | empty |
| 3 | 125 | 0.60 | 0.85 | 28 | empty |
| 4 | 176 | 0.49 | 0.77 | 23 | empty |
| 5 | 91 | 0.44 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2614 Ų buried · 19 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 5LHI · PDBe 5LHI · UniProt O60341 · UniProt Q9UKL0
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