4URA

Crystal structure of human JMJD2A in complex with compound 14a

• PDB DOI: https://doi.org/10.2210/pdb4URA/pdb

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


• Deposited: 2014-06-27 Released: 2015-06-17 
• Deposition Author(s): Krojer, T., England, K.S., Vollmar, M., Crawley, L., Williams, E., Riesebos, E., Szykowska, A., Burgess-Brown, N., Oppermann, U., Brennan, P.E., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.259 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor.

England, K.S., Tumber, A., Krojer, T., Scozzafava, G., Ng, S.S., Daniel, M., Szykowska, A., Che, K., von Delft, F., Burgess-Brown, N.A., Kawamura, A., Schofield, C.J., Brennan, P.E.

(2014) Medchemcomm 5: 1879-1886

• PubMed: 26682034 
• DOI: https://doi.org/10.1039/C4MD00291A
• Primary Citation of Related Structures:  
  4URA


• PubMed Abstract: 
  

  A potent inhibitor of the JmjC histone lysine demethylase KDM2A (compound 35 , pIC ₅₀ 7.2) with excellent selectivity over representatives from other KDM subfamilies has been developed; the discovery that a triazolopyridine compound binds to the active site of JmjC KDMs was followed by optimisation of the triazole substituent for KDM2A inhibition and selectivity.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK.

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: 84.59 kDa 
• Atom Count: 5,767 
• Modelled Residue Count: 693 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	360	Homo sapiens	Mutation(s): 0  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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEL	G [auth A], K [auth B]	2-(2H-1,2,3-triazol-4-yl)pyridine-4-carboxylic acid C8 H6 N4 O2 XGBRXPYFGYDEMS-UHFFFAOYSA-N
SO4	D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	E [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.259 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.04	α = 90
b = 149.66	β = 90
c = 57.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Krojer, T., England, K.S., Vollmar, M., Crawley, L., Williams, E., Riesebos, E., Szykowska, A., Burgess-Brown, N., Oppermann, U., Brennan, P.E., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2017-01-18
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other