2VD7

Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitor Scaffolds for 2-Oxoglutarate-Dependent Histone Lysine Demethylases.

Rose, N.R.Ng, S.S.Mecinovic, J.Lienard, B.M.R.Bello, S.H.Sun, Z.Mcdonough, M.A.Oppermann, U.Schofield, C.J.

(2008) J.Med.Chem. 51: 7053

  • DOI: 10.1021/jm800936s

  • PubMed Abstract: 
  • The dynamic methylation of histone lysyl residues plays an important role in biology by regulating transcription, maintaining genomic integrity, and by contributing to epigenetic effects. Here we describe a variety of inhibitor scaffolds that inhibit ...

    The dynamic methylation of histone lysyl residues plays an important role in biology by regulating transcription, maintaining genomic integrity, and by contributing to epigenetic effects. Here we describe a variety of inhibitor scaffolds that inhibit the human 2-oxoglutarate-dependent JMJD2 subfamily of histone demethylases. Combined with structural data, these chemical starting points will be useful to generate small-molecule probes to analyze the physiological roles of these enzymes in epigenetic signaling.


    Organizational Affiliation

    The Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A
A, B
381Homo sapiensGene 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 3 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
PD2
Query on PD2

Download SDF File 
Download CCD File 
A, B
PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PD2IC50: 4200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.285α = 90.00
b = 149.121β = 90.00
c = 57.566γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
REFMACphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-12-11
    Type: Database references, Derived calculations