5F5A

Crystal Structure of human JMJD2D complexed with KDOAM16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.

Bavetsias, V.Lanigan, R.M.Ruda, G.F.Atrash, B.McLaughlin, M.G.Tumber, A.Mok, N.Y.Le Bihan, Y.V.Dempster, S.Boxall, K.J.Jeganathan, F.Hatch, S.B.Savitsky, P.Velupillai, S.Krojer, T.England, K.S.Sejberg, J.Thai, C.Donovan, A.Pal, A.Scozzafava, G.Bennett, J.M.Kawamura, A.Johansson, C.Szykowska, A.Gileadi, C.Burgess-Brown, N.A.von Delft, F.Oppermann, U.Walters, Z.Shipley, J.Raynaud, F.I.Westaway, S.M.Prinjha, R.K.Fedorov, O.Burke, R.Schofield, C.J.Westwood, I.M.Bountra, C.Muller, S.van Montfort, R.L.Brennan, P.E.Blagg, J.

(2016) J.Med.Chem. 59: 1388-1409

  • DOI: 10.1021/acs.jmedchem.5b01635
  • Primary Citation of Related Structures:  5F2S, 5F2W, 5F32, 5F37, 5F39, 5F3C, 5F3E, 5F3G, 5F3I, 5F5C, 5F5I, 5FPL

  • PubMed Abstract: 
  • We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N ...

    We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , 15 Cotswold Road, London SM2 5NG, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 4D
A
346Homo sapiensGene Names: KDM4D (JHDM3D, JMJD2D)
EC: 1.14.11.-
Find proteins for Q6B0I6 (Homo sapiens)
Go to Gene View: KDM4D
Go to UniProtKB:  Q6B0I6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
5V0
Query on 5V0

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Download CCD File 
A
2-[(furan-2-ylmethylamino)methyl]pyridine-4-carboxylic acid
C12 H12 N2 O3
WAXTXDDUSDCZNA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.131 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.280α = 90.00
b = 71.280β = 90.00
c = 150.360γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2016-09-14
    Type: Structure summary