5FJH

Crystal structure of human JMJD2C catalytic domain in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino) -2-oxoethyl)amino)methyl)isonicotinic acid

• PDB DOI: https://doi.org/10.2210/pdb5FJH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-09 Released: 2015-10-21 
• Deposition Author(s): Cecatiello, V., Pasqualato, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal Structures of Human Jmjd2C Catalytic Domain Bound to Inhibitors

Cecatiello, V., Pasqualato, S.

To be published.

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: 82.03 kDa 
• Atom Count: 6,082 
• Modelled Residue Count: 676 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4C	A, B	349	Homo sapiens	Mutation(s): 0  EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3R0 (Homo sapiens) Explore Q9H3R0  Go to UniProtKB:  Q9H3R0
PHAROS:  Q9H3R0 GTEx:  ENSG00000107077

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMK	D [auth A], I [auth B]	2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid C15 H22 N4 O3 RTKGUAPXWDCFNW-BQYQJAHWSA-N
ZN	E [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	C [auth A], H [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	F [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.24	α = 90
b = 95.92	β = 90
c = 100.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Cecatiello, V., Pasqualato, S.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description