5ANQ

inhibitors of JumonjiC domain-containing histone demethylases

• PDB DOI: https://doi.org/10.2210/pdb5ANQ/pdb

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


• Deposited: 2015-09-07 Released: 2016-03-23 
• Deposition Author(s): Roatsch, M., Robaa, D., Pippel, M., Nettleship, J.E., Reddivari, Y., Bird, L.E., Hoffmann, I., Franz, H., Owens, R.J., Schuele, R., Flaig, R., Sippl, W., Jung, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Substituted 2-(2-Aminopyrimidin-4-Yl)Pyridine-4-Carboxylates as Potent Inhibitors of Jumonjic Domain-Containing Histone Demethylases.

Roatsch, M., Robaa, D., Pippel, M., Nettleship, J.E., Reddivari, Y., Bird, L.E., Hoffmann, I., Franz, H., Owens, R.J., Schole, R., Flaig, R., Sippl, W., Jung, M.

(2016) Future Med Chem 8: 1553

• PubMed: 26971619 
• DOI: https://doi.org/10.4155/fmc.15.188
• Primary Citation of Related Structures:  
  5ANQ


• PubMed Abstract: 
  

  Aberrant expression of iron(II)- and 2-oxoglutarate-dependent JumonjiC histone demethylases has been linked to cancer. Potent demethylase inhibitors are drug candidates and biochemical tools to elucidate the functional impact of demethylase inhibition.

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Organizational Affiliation: 

Albert-Ludwigs-University Freiburg, Institute of Pharmaceutical Sciences, Albertstraße 25, 79104 Freiburg i.Br., Germany.

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: 84.92 kDa 
• Atom Count: 6,125 
• Modelled Residue Count: 694 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	359	Homo sapiens	Mutation(s): 0  EC: 1.14.11.27
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
5YQ	C [auth A], I [auth B]	2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid C16 H13 N5 O2 YUSWODBVCDCVMS-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	D [auth A], J [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	H [auth A], N [auth B], O [auth B], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
5YQ	Binding MOAD:  5ANQ	IC50: 3980 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.232 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.694	α = 90
b = 149.271	β = 90
c = 57.527	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Roatsch, M., Robaa, D., Pippel, M., Nettleship, J.E., Reddivari, Y., Bird, L.E., Hoffmann, I., Franz, H., Owens, R.J., Schuele, R., Flaig, R., Sippl, W., Jung, M.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description