5LY2

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5LY1, 5LY2

  • 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 selectivity over other KDMs/2OG oxygenases, including closely related KDM4D/E isoforms ...

    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

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4AA, B, C, D381Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
PHAROS:  O75164
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CP2_R6Kme3E, F, G, H14artificial sequencesMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OGA
Query on OGA

Download Ideal Coordinates CCD File 
DA [auth D], K [auth A], R [auth B], Y [auth C]N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], S [auth B], T [auth B], U [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D], J [auth A], P [auth B], W [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth D], I [auth A], O [auth B], V [auth C]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth D], N [auth B], Q [auth B], X [auth C], Z [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E, F, G, HL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
OGA BindingDB:  5LY2 IC50: min: 8.50e+4, max: 2.50e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.306α = 90
b = 103.747β = 99.14
c = 142.367γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary