7JM5 | pdb_00007jm5

Crystal structure of KDM4B in complex with QC6352

• PDB DOI: https://doi.org/10.2210/pdb7JM5/pdb

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


• Deposited: 2020-07-31 Released: 2022-02-02 
• Deposition Author(s): White, S.W., Yun, M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Targeting KDM4 for treating PAX3-FOXO1-driven alveolar rhabdomyosarcoma.

Singh, S., Abu-Zaid, A., Jin, H., Fang, J., Wu, Q., Wang, T., Feng, H., Quarni, W., Shao, Y., Maxham, L., Abdolvahabi, A., Yun, M.K., Vaithiyalingam, S., Tan, H., Bowling, J., Honnell, V., Young, B., Guo, Y., Bajpai, R., Pruett-Miller, S.M., Grosveld, G.C., Hatley, M., Xu, B., Fan, Y., Wu, G., Chen, E.Y., Chen, T., Lewis, P.W., Rankovic, Z., Li, Y., Murphy, A.J., Easton, J., Peng, J., Chen, X., Wang, R., White, S.W., Davidoff, A.M., Yang, J.

(2022) Sci Transl Med 14: eabq2096-eabq2096

• PubMed: 35857643 
• DOI: https://doi.org/10.1126/scitranslmed.abq2096
• Primary Citation Related Structures: 
  7JM5


• PubMed Abstract: 
  

  Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3-Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1 ⁺ RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1-governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1 ⁺ RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1-related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.

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Organizational Affiliation: 
• Department of Surgery, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.
Department of Orthopedics, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China.
Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Protein Technologies Center, Molecular Interaction Analysis, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Biostatistics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Genetics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.
Department of Pathology, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Ave., Suite 500, Memphis, TN 38163, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.38 kDa 
• Atom Count: 5,631 
• Modeled Residue Count: 682 
• Deposited Residue Count: 734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4B	A, B	367	Homo sapiens	Mutation(s): 0  Gene Names: KDM4B, JHDM3B, JMJD2B, KIAA0876 EC: 1.14.11.66
UniProt & NIH Common Fund Data Resources
Find proteins for O94953 (Homo sapiens) Explore O94953  Go to UniProtKB:  O94953
PHAROS:  O94953 GTEx:  ENSG00000127663

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9DJ (Subject of Investigation/LOI)	D [auth A], G [auth B]	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
ZN	F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9DJ	BindingDB:  7JM5	IC50: min: 35, max: 56 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.244 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.825	α = 90
b = 97.107	β = 106.516
c = 80.068	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): White, S.W., Yun, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA229739

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-08-17
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary