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Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (N10057a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

Source organism: Homo sapiens
Biochemical function: not assigned
Biological process: not assigned
Cellular component: not assigned

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EC 1.14.11.67: [Histone H3]-trimethyl-L-lysine(4) demethylase

Reaction catalysed:
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Systematic name:
[Histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4),2-oxoglutarate:oxygen oxidoreductase

GO terms

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Sequence families

Pfam Protein families (Pfam)
PF02928
Domain description: C5HC2 zinc finger
Occurring in:
  1. Lysine-specific demethylase 5B
The deposited structure of PDB entry 5fz4 contains 1 copy of Pfam domain PF02928 (C5HC2 zinc finger) in Lysine-specific demethylase 5B. Showing 1 copy in chain A.

PF21323
Domain description: Lysine-specific demethylase 5, C-terminal helical domain
Occurring in:
  1. Lysine-specific demethylase 5B
The deposited structure of PDB entry 5fz4 contains 1 copy of Pfam domain PF21323 (Lysine-specific demethylase 5, C-terminal helical domain) in Lysine-specific demethylase 5B. Showing 1 copy in chain A.

PF02373
Domain description: JmjC domain, hydroxylase
Occurring in:
  1. Lysine-specific demethylase 5B
The deposited structure of PDB entry 5fz4 contains 1 copy of Pfam domain PF02373 (JmjC domain, hydroxylase) in Lysine-specific demethylase 5B. Showing 1 copy in chain A.

PF02375
Domain description: jmjN domain
Occurring in:
  1. Lysine-specific demethylase 5B
The deposited structure of PDB entry 5fz4 contains 1 copy of Pfam domain PF02375 (jmjN domain) in Lysine-specific demethylase 5B. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR003349
Domain description: JmjN domain
Occurring in:
  1. Lysine-specific demethylase 5B
IPR003347
Domain description: JmjC domain
Occurring in:
  1. Lysine-specific demethylase 5B
IPR004198
Domain description: Zinc finger, C5HC2-type
Occurring in:
  1. Lysine-specific demethylase 5B

Structure domain

CATH CATH domain
2.60.120.650
Class: Mainly Beta
Architecture: Sandwich
Topology: Jelly Rolls
Homology: Cupin
Occurring in:
  1. Lysine-specific demethylase 5B
The deposited structure of PDB entry 5fz4 contains 1 copy of CATH domain 2.60.120.650 (Jelly Rolls) in Lysine-specific demethylase 5B. Showing 1 copy in chain A.

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