MolNFT v1 · #125722 · protein
Structure of the KDM1A/COREST complex with the inhibitor 4-ethyl-N-[3- (methoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3- YL]METHOXY]PHENOXY]METHYL]PHENYL]THIENO[3,2-B]PYRROLE-5-carboxamide
5LHH · Lysine-specific histone demethylase 1A: “Structure of the KDM1A/COREST complex with the inhibitor 4-ethyl-N-[3…”. X-ray diffraction, 2 ligands (FAD, 6X0), 9 pockets (best druggability 0.82). MolNFT v1 #125722 on GenesisL1: 3D…
- PDB
- 5LHH
- 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
- FAD, 6X0
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 666 | 43% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 133 | 62% helix, 0% strand | Q9UKL0 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- 6X0 · 4-ethyl-~{N}-[3-(methoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide · ligand · chains A
- GOL · Glycerol · additive · 6 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 | 1058 | 0.82 | 0.83 | 90 | FAD, GOL, 6X0 |
| 2 | 333 | 0.60 | 0.77 | 35 | empty |
| 3 | 206 | 0.48 | 0.75 | 23 | empty |
| 4 | 95 | 0.46 | 0.79 | 19 | empty |
| 5 | 137 | 0.44 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2772 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 5LHH · PDBe 5LHH · UniProt O60341 · UniProt Q9UKL0
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