5ANQ | pdb_00005anq

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 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

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 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. Virtual screening identified a novel lead scaffold against JMJD2A with low-micromolar potency in vitro. Analogs were acquired from commercial sources respectively synthesized in feedback with biological testing. Optimized compounds were transformed into cell-permeable prodrugs. A cocrystal x-ray structure revealed the mode of binding of these compounds as competitive to 2-oxoglutarate and confirmed kinetic experiments. Selectivity studies revealed a preference for JMJD2A and JARID1A over JMJD3. Virtual screening and rational structural optimization led to a novel scaffold for highly potent and selective JMJD2A inhibitors.

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Organizational Affiliation: 
• Albert-Ludwigs-University Freiburg, Institute of Pharmaceutical Sciences, Albertstraße 25, 79104 Freiburg i.Br., Germany.
Martin-Luther-University Halle-Wittenberg, Institute of Pharmacy, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany.
Oxford Protein Production Facility UK (OPPF-UK), Rutherford Appleton Laboratory, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK.
University Medical Center Freiburg, Central Clinical Research, Breisacher Straße 66, 79106 Freiburg i.Br., Germany.
Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire, OX11 0DE, 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: 84.92 kDa 
• Atom Count: 6,125 
• Modeled 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 (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
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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.232 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

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