5VMP

Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714

• PDB DOI: https://doi.org/10.2210/pdb5VMP/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-28 Released: 2017-09-27 
• Deposition Author(s): Hosfield, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.260 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 

Starting Model: experimental

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

• PubMed: 28835804 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 173.65 kDa 
• Atom Count: 11,619 
• Modelled Residue Count: 1,370 
• Deposited Residue Count: 1,476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B, C, D	369	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11 (PDB Primary Data), 1.14.11.66 (UniProt), 1.14.11.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164  Go to UniProtKB:  O75164
PHAROS:  O75164 GTEx:  ENSG00000066135

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9FJ	G [auth A], J [auth B], M [auth C], P [auth D]	3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid C18 H20 N2 O3 NXQKMWGCRMQRSS-ZDUSSCGKSA-N
ZN	F [auth A], I [auth B], L [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	E [auth A], H [auth B], K [auth C], N [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.260 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.14	α = 90
b = 101.429	β = 99.85
c = 142.673	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description