Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47091.24 
• Atom Count: 2992 
• Residue Count: 397 
• Unique protein chains: 1

3U78

E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 Jumonji demethylase

• DOI: 10.2210/pdb3U78/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2011-10-13 Released: 2012-01-25 
• Deposition Author(s): Upadhyay, A.K., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.689 Å
• R-Value Free: 0.265 
• R-Value Work: 0.198 

Literature

An Analog of BIX-01294 Selectively Inhibits a Family of Histone H3 Lysine 9 Jumonji Demethylases.

Upadhyay, A.K., Rotili, D., Han, J.W., Hu, R., Chang, Y., Labella, D., Zhang, X., Yoon, Y.S., Mai, A., Cheng, X.

(2012) J.Mol.Biol. 416: 319-327

• PubMed: 22227394 
• DOI: 10.1016/j.jmb.2011.12.036


• PubMed Abstract: 
  

BIX-01294 and its analogs were originally identified and subsequently designed as potent inhibitors against histone H3 lysine 9 (H3K9) methyltransferases G9a and G9a-like protein. Here, we show that BIX-01294 and its analog E67 can also inhibit H3K9 Jumonji demethylase KIAA1718 with half-maximal inhibitory concentrations in low micromolar range. Crystallographic analysis of KIAA1718 Jumonji domain in complex with E67 indicated that the benzylated six-membered piperidine ring was disordered and exposed to solvent. Removing the moiety (generating compound E67-2) has no effect on the potency against KIAA1718 but, unexpectedly, lost inhibition against G9a-like protein by a factor of 1500. Furthermore, E67 and E67-2 have no effect on the activity against histone H3 lysine 4 (H3K4) demethylase JARID1C. Thus, our study provides a new avenue for designing and improving the potency and selectivity of inhibitors against H3K9 Jumonji demethylases over H3K9 methyltransferases and H3K4 demethylases.

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Organizational Affiliation: 

Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific demethylase 7	A	397	Homo sapiens	Mutation(s): 0  Gene Names: KDM7A (JHDM1D, KDM7, KIAA1718) EC: 1.14.11.-
Find proteins for Q6ZMT4 (Homo sapiens) Go to Gene View: KDM7A Go to UniProtKB:  Q6ZMT4

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
AKG	A	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
E67	A	7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine C31 H47 N7 O2 KJNBMUDJPFXUTG-UHFFFAOYSA-N
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
E67	Ki: 2500 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.689 Å
• R-Value Free: 0.265 
• R-Value Work: 0.198 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 77.429	α = 90.00
b = 77.429	β = 90.00
c = 289.685	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	data collection
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-10-13 
• Released Date: 2012-01-25 
• Deposition Author(s): Upadhyay, A.K., Cheng, X.

Revision History 

• Version 1.0: 2012-01-25
  Type: Initial release
• Version 1.1: 2012-02-22
  Type: Database references