5ISL

Linked KDM5A Jmj Domain Bound to the Inhibitor C49 (2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.

Horton, J.R.Liu, X.Gale, M.Wu, L.Shanks, J.R.Zhang, X.Webber, P.J.Bell, J.S.Kales, S.C.Mott, B.T.Rai, G.Jansen, D.J.Henderson, M.J.Urban, D.J.Hall, M.D.Simeonov, A.Maloney, D.J.Johns, M.A.Fu, H.Jadhav, A.Vertino, P.M.Yan, Q.Cheng, X.

(2016) Cell Chem Biol 23: 769-781

  • DOI: 10.1016/j.chembiol.2016.06.006
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DQF, 6DQE, 6DQD, 6DQC, 6DQB, 6DQA, 6DQ9, 6DQ8, 6DQ7, 6DQ6, 6DQ5, 6DQ4, 6BH5, 6BH4, 6BH3, 6BH2, 6BH1, 6BH0, 6BGZ, 6BGY, 6BGX, 6BGW, 6BGV, 6BGU

  • PubMed Abstract: 
  • The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inh ...

    The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.


    Related Citations: 
    • Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases.
      Horton, J.R.,Engstrom, A.,Zoeller, E.L.,Liu, X.,Shanks, J.R.,Zhang, X.,Johns, M.A.,Vertino, P.M.,Fu, H.,Cheng, X.
      (2016) J. Biol. Chem. 291: 2631


    Organizational Affiliation

    Department of Biochemistry, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA. Electronic address: xcheng@emory.edu.,Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.,National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA.,Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA. Electronic address: qin.yan@yale.edu.,Department of Biochemistry, Emory University, Atlanta, GA 30322, USA.,Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.,Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA.,Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A
A
330Homo sapiensMutation(s): 0 
Gene Names: KDM5A (JARID1A, RBBP2, RBP2)
EC: 1.14.11.-
Find proteins for P29375 (Homo sapiens)
Go to Gene View: KDM5A
Go to UniProtKB:  P29375
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MMK
Query on MMK

Download SDF File 
Download CCD File 
A
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
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMKKd: 52 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.144α = 90.00
b = 61.771β = 92.48
c = 46.700γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM114306-01

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-25
    Type: Author supporting evidence