5FP9

Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.5b01537
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN LYSINE-SPECIFIC DEMETHYLASE 4D JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D, JMJD2D
A
334Homo sapiensMutation(s): 0 
Gene Names: KDM4DJHDM3DJMJD2D
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt)
Find proteins for Q6B0I6 (Homo sapiens)
Go to UniProtKB:  Q6B0I6
NIH Common Fund Data Resources
PHAROS  Q6B0I6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4SV
Query on 4SV

Download CCD File 
A
3-AMINOPYRIDINE-4-CARBOXYLIC ACID
C6 H6 N2 O2
FYEQKMAVRYRMBL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4SVIC50:  1259   nM  BindingDB
4SVIC50:  1585   nM  Binding MOAD
4SVIC50:  1585   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.416α = 90
b = 71.416β = 90
c = 150.292γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-11-27 
  • Released Date: 2016-01-27 
  • Deposition Author(s): Chung, C.

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references