› 3abt

X-ray diffraction
3.2Å resolution

Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine

Released:
DOI: 10.2210/pdb3abt/pdb
PDB entry 3abt coloured by chain, front view.
PDB entry 3abt coloured by chain, side view.
PDB entry 3abt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structurally designed trans-2-phenylcyclopropylamine derivatives potently inhibit histone demethylase LSD1/KDM1 .
Mimasu S, Umezawa N, Sato S, Higuchi T, Umehara T, Yokoyama S
Biochemistry 49 6494-503 (2010)
PMID: 20568732

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129945 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific histone demethylase 1A Chain: A
Molecule details ›
Chain: A
Length: 662 amino acids
Theoretical weight: 73.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O60341 (Residues: 172-833; Coverage: 78%)
Gene names: AOF2, KDM1, KDM1A, KIAA0601, LSD1
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 2PF 1 x 2PF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU, SPRING-8 BEAMLINE BL26B2
Spacegroup: P6122
Unit cell:
a: 183.84Å b: 183.84Å c: 109.15Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.231 0.231 0.272
Expression system: Escherichia coli BL21

Quick links

Citations

27 review citations

Epigenetic protein families: a new frontier for drug discovery.
Arrowsmith et al. (2012)
26 more

8 mentions without citation

Targeting histone lysine demethylases - progress, challenges, and the future.
Thinnes et al. (2014)
7 more