ISDA

Deposition Date 2017-04-11

Release Date 2017-09-27

Last Version Date 2024-03-13

Entry Detail

PDB ID:

5VGI

Keywords:

OXIDOREDUCTASE/INHIBITOR

Title:

Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.07 Å

R-Value Free:

0.24

R-Value Work:

0.18

R-Value Observed:

0.19

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Lysine-specific demethylase 4A
Gene (Uniprot):KDM4A
Chain IDs:A, B, C, D
Chain Length:370
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:O75164 Pfam ID:PF02375, PF02373 EC:1.14.11.27

Ligand Molecules

9DJ

Primary Citation

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.Show

ACS Med Chem Lett 8 869 874 (2017)

PMID: 28835804 DOI: 10.1021/acsmedchemlett.7b00220

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures