5FPL

Crystal structure of human JARID1B in complex with CCT363901

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 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., 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.M., Brennan, P.E., Blagg, J.

(2016) J Med Chem 59: 1388

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

  • 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-met ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B A480Homo sapiensMutation(s): 0 
Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1
EC: 1.14.11.67
Find proteins for Q9UGL1 (Homo sapiens)
Explore Q9UGL1 
Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS:  Q9UGL1
GTEx:  ENSG00000117139
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QAY
Query on QAY
Download Ideal Coordinates CCD File 
A
8-[4-(2-azanylethyl)pyrazol-1-yl]-3H-pyrido[3,4-d]pyrimidin-4-one
C12 H12 N6 O
YNSLRVQPGFUMPO-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.91α = 90
b = 142.91β = 90
c = 152.1γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2018-01-24
    Changes: Database references