5F5I

Crystal Structure of human JMJD2A complexed with KDOOA011340


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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
  • Structures With Same Primary Citation

  • 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 4A
A, B
363Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11
Find proteins for O75164 (Homo sapiens)
Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS  O75164
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5V1
Query on 5V1

Download CCD File 
A, B
2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid
C14 H14 N2 O2
IBSVWTKUXPGZFI-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.03α = 90
b = 149.58β = 90
c = 57.92γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2016-09-14
    Changes: Structure summary