7EQV

Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid

• PDB DOI: https://doi.org/10.2210/pdb7EQV/pdb

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


• Deposited: 2021-05-04 Released: 2022-05-18 
• Deposition Author(s): Fang, W.-K., Yang, S.-M., Wang, W.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 

Literature

Natural product myricetin is a pan-KDM4 inhibitor which with poly lactic-co-glycolic acid formulation effectively targets castration-resistant prostate cancer.

Liu, J.S., Fang, W.K., Yang, S.M., Wu, M.C., Chen, T.J., Chen, C.M., Lin, T.Y., Liu, K.L., Wu, C.M., Chen, Y.C., Chuu, C.P., Wang, L.Y., Hsieh, H.P., Kung, H.J., Wang, W.C.

(2022) J Biomed Sci 29: 29-29

• PubMed: 35534851 
• DOI: https://doi.org/10.1186/s12929-022-00812-3
• Primary Citation of Related Structures:  
  7EQV


• PubMed Abstract: 
  

  Castration-resistant prostate cancer (CRPC) with sustained androgen receptor (AR) signaling remains a critical clinical challenge, despite androgen depletion therapy. The Jumonji C-containing histone lysine demethylase family 4 (KDM4) members, KDM4A‒KDM4C, serve as critical coactivators of AR to promote tumor growth in prostate cancer and are candidate therapeutic targets to overcome AR mutations/alterations-mediated resistance in CRPC.

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Organizational Affiliation: 

Institute of Molecular and Cellular Biology and Department of Life Sciences, National Tsing-Hua University, Hsinchu, 30013, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 40.89 kDa 
• Atom Count: 2,963 
• Modelled Residue Count: 340 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A	348	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11.66 (PDB Primary Data), 1.14.11.69 (PDB Primary Data)
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHB (Subject of Investigation/LOI)	B [auth A]	3,4-DIHYDROXYBENZOIC ACID C7 H6 O4 YQUVCSBJEUQKSH-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.168 
• R-Value Observed: 0.171 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.396	α = 90
b = 149.396	β = 90
c = 62.175	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-05-18 
Deposition Author(s): Fang, W.-K., Yang, S.-M., Wang, W.-C.

Revision History  

• Version 1.0: 2022-05-18
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description