› 4uf0

X-ray diffraction
1.78Å resolution

Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.

Released:
DOI: 10.2210/pdb4uf0/pdb
PDB entry 4uf0 coloured by chain, front view.
PDB entry 4uf0 coloured by chain, side view.
PDB entry 4uf0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of human KDM5B guides histone demethylase inhibitor development.
Johansson C, Velupillai S, Tumber A, Szykowska A, Hookway ES, Nowak RP, Strain-Damerell C, Gileadi C, Philpott M, Burgess-Brown N, Wu N, Kopec J, Nuzzi A, Steuber H, Egner U, Badock V, Munro S, LaThangue NB, Westaway S, Brown J, Athanasou N, Prinjha R, Brennan PE, Oppermann U
Nat Chem Biol 12 539-45 (2016)
PMID: 27214403

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(27) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(27) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127019 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone demethylase UTY Chain: A
Molecule details ›
Chain: A
Length: 478 amino acids
Theoretical weight: 55.02 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O14607 (Residues: 878-1347; Coverage: 35%)
Gene names: KDM6C, UTY
Sequence domains:
Structure domains:
Histone demethylase UTY Chain: B
Molecule details ›
Chain: B
Length: 478 amino acids
Theoretical weight: 55.01 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O14607 (Residues: 878-1347; Coverage: 35%)
Gene names: KDM6C, UTY
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand FE2 2 x FE2
Ligand MMK 2 x MMK
Ligand ZN 2 x ZN
Ligand EDO 20 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 90.494Å b: 110.458Å c: 119.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.152 0.149 0.215
Expression system: Spodoptera frugiperda

Quick links

Citations

24 review citations

The great escape: tumour cell plasticity in resistance to targeted therapy.
Boumahdi et al. (2020)
23 more

1 mention without citation

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)