5FP3

Cell penetrant inhibitors of the JMJD2 (KDM4) and JARID1 (KDM5) families of histone lysine demethylases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.

Westaway, S.M.Preston, A.G.S.Barker, M.D.Brown, F.Brown, J.A.Campbell, M.Chung, C.Diallo, H.Douault, C.Drewes, G.Eagle, R.Gordon, L.Haslam, C.Hayhow, T.G.Humphreys, P.G.Joberty, G.Katso, R.Kruidenier, L.Leveridge, M.Liddle, J.Mosley, J.Muelbaier, M.Randle, R.Rioja, I.Rueger, A.Seal, G.A.Sheppard, R.J.Singh, O.Taylor, J.Thomas, P.Thomson, D.Wilson, D.M.Lee, K.Prinjha, R.K.

(2016) J Med Chem 59: 1357

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01537
  • Primary Citation of Related Structures:  
    5FP3, 5FP4, 5FP8, 5FP9, 5FPA, 5FPB

  • PubMed Abstract: 

    Optimization of KDM6B (JMJD3) HTS hit 12 led to the identification of 3-((furan-2-ylmethyl)amino)pyridine-4-carboxylic acid 34 and 3-(((3-methylthiophen-2-yl)methyl)amino)pyridine-4-carboxylic acid 39 that are inhibitors of the KDM4 (JMJD2) family of histone lysine demethylases. Compounds 34 and 39 possess activity, IC50 ≤ 100 nM, in KDM4 family biochemical (RFMS) assays with ≥ 50-fold selectivity against KDM6B and activity in a mechanistic KDM4C cell imaging assay (IC50 = 6-8 μM). Compounds 34 and 39 are also potent inhibitors of KDM5C (JARID1C) (RFMS IC50 = 100-125 nM).


  • Organizational Affiliation

    Epinova Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D , Stevenage SG1 2NY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HUMAN LYSINE-SPECIFIC DEMETHYLASE 6B, JMJD3
A, B
510Homo sapiensMutation(s): 0 
EC: 1.14.11 (PDB Primary Data), 1.14.11.68 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15054 (Homo sapiens)
Explore O15054 
Go to UniProtKB:  O15054
PHAROS:  O15054
GTEx:  ENSG00000132510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15054
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YC8
Query on YC8

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
3-(4-phenylbutanoylamino)pyridine-4-carboxylic acid
C16 H16 N2 O3
FLWYUGQMDDTDDS-UHFFFAOYSA-N
BCN
Query on BCN

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B],
N [auth B]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A],
L [auth B],
O [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.199α = 85.59
b = 65.552β = 67.65
c = 77.301γ = 68.39
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-01-27 
  • Deposition Author(s): Chung, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 2.0: 2018-03-07
    Changes: Atomic model, Derived calculations, Non-polymer description
  • Version 3.0: 2019-10-30
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 3.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations