5LY1

JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.

Kawamura, A.Munzel, M.Kojima, T.Yapp, C.Bhushan, B.Goto, Y.Tumber, A.Katoh, T.King, O.N.Passioura, T.Walport, L.J.Hatch, S.B.Madden, S.Muller, S.Brennan, P.E.Chowdhury, R.Hopkinson, R.J.Suga, H.Schofield, C.J.

(2017) Nat Commun 8: 14773-14773

  • DOI: 10.1038/ncomms14773
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The JmjC histone demethylases (KDMs) are linked to tumour cell proliferation and are current cancer targets; however, very few highly selective inhibitors for these are available. Here we report cyclic peptide inhibitors of the KDM4A-C with selectivi ...

    The JmjC histone demethylases (KDMs) are linked to tumour cell proliferation and are current cancer targets; however, very few highly selective inhibitors for these are available. Here we report cyclic peptide inhibitors of the KDM4A-C with selectivity over other KDMs/2OG oxygenases, including closely related KDM4D/E isoforms. Crystal structures and biochemical analyses of one of the inhibitors (CP2) with KDM4A reveals that CP2 binds differently to, but competes with, histone substrates in the active site. Substitution of the active site binding arginine of CP2 to N-ɛ-trimethyl-lysine or methylated arginine results in cyclic peptide substrates, indicating that KDM4s may act on non-histone substrates. Targeted modifications to CP2 based on crystallographic and mass spectrometry analyses results in variants with greater proteolytic robustness. Peptide dosing in cells manifests KDM4A target stabilization. Although further development is required to optimize cellular activity, the results reveal the feasibility of highly selective non-metal chelating, substrate-competitive inhibitors of the JmjC KDMs.


    Related Citations: 
    • Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
      Ng, S.S.,Kavanagh, K.L.,McDonough, M.A.,Butler, D.,Pilka, E.S.,Lienard, B.M.,Bray, J.E.,Savitsky, P.,Gileadi, O.,von Delft, F.,Rose, N.R.,Offer, J.,Scheinost, J.C.,Borowski, T.,Sundstrom, M.,Schofield, C.J.,Oppermann, U.
      (2007) Nature 448: 87
    • Substrate- and cofactor-independent inhibition of histone demethylase KDM4C.
      Leurs, U.,Lohse, B.,Rand, K.D.,Ming, S.,Riise, E.S.,Cole, P.A.,Kristensen, J.L.,Clausen, R.P.
      (2014) ACS Chem. Biol. 9: 2131


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan.,JST, CREST, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan.,Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington OX3 7DQ, UK.,Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.,Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4A
A, B, C, D
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CP2
E
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

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

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Download CCD File 
A, B, D
PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
48V
Query on 48V
E
peptide-likeC5 H10 N2 O3 S

--

DTY
Query on DTY
E
D-PEPTIDE LINKINGC9 H11 N O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.265α = 90.00
b = 101.482β = 99.56
c = 140.330γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references