4AI9

JMJD2A Complexed with Daminozide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.

Rose, N.R.Woon, E.C.Tumber, A.Walport, L.J.Chowdhury, R.Li, X.S.King, O.N.Lejeune, C.Ng, S.S.Krojer, T.Chan, M.C.Rydzik, A.M.Hopkinson, R.J.Che, K.H.Daniel, M.Strain-Damerell, C.Gileadi, C.Kochan, G.Leung, I.K.Dunford, J.Yeoh, K.K.Ratcliffe, P.J.Burgess-Brown, N.von Delft, F.Muller, S.Marsden, B.Brennan, P.E.McDonough, M.A.Oppermann, U.Klose, R.J.Schofield, C.J.Kawamura, A.

(2012) J. Med. Chem. 55: 6639-6643

  • DOI: 10.1021/jm300677j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related ox ...

    The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related oxygenases. Results led to the finding that daminozide (N-(dimethylamino)succinamic acid, 160 Da), a plant growth regulator, selectively inhibits the KDM2/7 JmjC subfamily. Kinetic and crystallographic studies reveal that daminozide chelates the active site metal via its hydrazide carbonyl and dimethylamino groups.


    Organizational Affiliation

    Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 4A
A, B
381Homo sapiensMutation(s): 0 
Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677)
EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens)
Go to Gene View: KDM4A
Go to UniProtKB:  O75164
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
DZA
Query on DZA

Download SDF File 
Download CCD File 
A, B
DAMINOZIDE
C6 H12 N2 O3
NOQGZXFMHARMLW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.476α = 90.00
b = 149.752β = 90.00
c = 57.533γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Database references, Structure summary
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation