5VGI

Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report



Literature

Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models.

Chen, Y.K.Bonaldi, T.Cuomo, A.Del Rosario, J.R.Hosfield, D.J.Kanouni, T.Kao, S.C.Lai, C.Lobo, N.A.Matuszkiewicz, J.McGeehan, A.O'Connell, S.M.Shi, L.Stafford, J.A.Stansfield, R.K.Veal, J.M.Weiss, M.S.Yuen, N.Y.Wallace, M.B.

(2017) ACS Med Chem Lett 8: 869-874

  • DOI: 10.1021/acsmedchemlett.7b00220
  • Primary Citation of Related Structures:  
    5VGI, 5VMP

  • PubMed Abstract: 
  • Histone lysine demethylases (KDMs) play a vital role in the regulation of chromatin-related processes. Herein, we describe our discovery of a series of potent KDM4 inhibitors that are both cell permeable and antiproliferative in cancer models. The mo ...

    Histone lysine demethylases (KDMs) play a vital role in the regulation of chromatin-related processes. Herein, we describe our discovery of a series of potent KDM4 inhibitors that are both cell permeable and antiproliferative in cancer models. The modulation of histone H3K9me3 and H3K36me3 upon compound treatment was verified by homogeneous time-resolved fluorescence assay and by mass spectroscopy detection. Optimization of the series using structure-based drug design led to compound 6 (QC6352), a potent KDM4 family inhibitor that is efficacious in breast and colon cancer PDX models.


    Organizational Affiliation

    Celgene Quanticel Research, 10300 Campus Point Drive, Suite 100, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 4AABCD370Homo sapiensMutation(s): 0 
Gene Names: KDM4AJHDM3AJMJD2JMJD2AKIAA0677
EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
Find proteins for O75164 (Homo sapiens)
Explore O75164 
Go to UniProtKB:  O75164
NIH Common Fund Data Resources
PHAROS  O75164
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9DJ
Query on 9DJ

Download CCD File 
A, B, C, D
3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid
C24 H25 N3 O2
XSMABFRQESMONQ-SFHVURJKSA-N
 Ligand Interaction
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.318α = 90
b = 101.594β = 99.64
c = 141.893γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-04-11 
  • Released Date: 2017-09-27 
  • Deposition Author(s): Hosfield, D.J.

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release