5FWJ

Crystal structure of human JARID1C in complex with KDM5-C49


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.

Johansson, C.Velupillai, S.Tumber, A.Szykowska, A.Hookway, E.S.Nowak, R.P.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, N.B.Westaway, S.Brown, J.Athanasou, N.Prinjha, R.Brennan, P.E.Oppermann, U.

(2016) Nat Chem Biol 12: 539

  • DOI: 10.1038/nchembio.2087
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal ...

    Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.


    Organizational Affiliation

    Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEMETHYLASE JARID1C
A, B
471Homo sapiensMutation(s): 0 
Gene Names: KDM5CDXS1272EJARID1CSMCXXE169
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for P41229 (Homo sapiens)
Go to UniProtKB:  P41229
NIH Common Fund Data Resources
PHAROS  P41229
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMK
Query on MMK

Download CCD File 
A, B
2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid
C15 H22 N4 O3
RTKGUAPXWDCFNW-BQYQJAHWSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMKKi:  6.099999904632568   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.96α = 86.71
b = 67.34β = 76.56
c = 74.73γ = 70.35
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-01
    Changes: Database references
  • Version 1.3: 2016-06-29
    Changes: Database references
  • Version 1.4: 2018-01-24
    Changes: Structure summary