› 6kgk

X-ray diffraction
2.7Å resolution

LSD1-CoREST-S2101 five-membered ring adduct model

Released:
DOI: 10.2210/pdb6kgk/pdb
PDB entry 6kgk coloured by chain, front view.
PDB entry 6kgk coloured by chain, side view.
PDB entry 6kgk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Niwa H, Sato S, Handa N, Sengoku T, Umehara T, Yokoyama S
ChemMedChem 15 787-793 (2020)
PMID: 32166890

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + acceptor + H(2)O = a [histone H3]-N(6)-methyl-L-lysine(4) + formaldehyde + reduced acceptor
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129967 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 669 amino acids
Theoretical weight: 74.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60341 (Residues: 172-833; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
REST corepressor 1 Chain: B
Molecule details ›
Chain: B
Length: 140 amino acids
Theoretical weight: 15.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli KRX
UniProt:
  • Canonical: Q9UKL0 (Residues: 311-443; Coverage: 27%)
Gene names: KIAA0071, RCOR, RCOR1
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 3 x GOL
Ligand DJ0 1 x DJ0
Ligand FAD 1 x FAD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: I222
Unit cell:
a: 119.545Å b: 178.549Å c: 234.194Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.206
Expression systems:
  • Escherichia coli
  • Escherichia coli KRX

Quick links

Citations

5 citation in other articles

MicroRNA-137-mediated inhibition of lysine-specific demethylase-1 prevents against rheumatoid arthritis in an association with the REST/mTOR axis.
Sun et al. (2021)
4 more

1 mention without citation

Monobenzone, a Novel and Potent KDM1A Inhibitor, Suppresses Migration of Gastric Cancer Cells.
Ma et al. (2021)