Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90462.80 
• Atom Count: 5643 
• Residue Count: 762 
• Unique protein chains: 1

5A80

Crystal structure of human JMJD2A in complex with compound 40

• DOI: 10.2210/pdb5A80/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2015-07-11 Released: 2016-01-13 
• Deposition Author(s): Nowak, R., Velupillai, S., Krojer, T., Gileadi, C., Johansson, C., Korczynska, M., Le, D.D., Younger, N., Gregori-Puigjane, E., Tumber, A., Iwasa, E., Pollock, S.B., Ortiz Torres, I., Kopec, J., Tallant, C., Froese, S., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Shoichet, B.K., Fujimori, D.G., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.249 
• R-Value Work: 0.190 

Literature

Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.

Korczynska, M., Le, D.D., Younger, N., Gregori-Puigjane, E., Tumber, A., Krojer, T., Velupillai, S., Gileadi, C., Nowak, R.P., Iwasa, E., Pollock, S.B., Ortiz Torres, I., Oppermann, U., Shoichet, B.K., Fujimori, D.G.

(2016) J.Med.Chem. 59: 1580

• PubMed: 26699912 
• DOI: 10.1021/acs.jmedchem.5b01527
• Primary Citation of Related Structures:  
  5A7W, 5A7S, 5A7Q, 5A7P, 5A7O, 5A7N


• PubMed Abstract: 
  

Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A (JHDM3A, JMJD2, JMJD2A, KIAA0677) EC: 1.14.11.-
Find proteins for O75164 (Homo sapiens) Go to Gene View: KDM4A Go to UniProtKB:  O75164

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
9CJ	A, B	2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid C21 H18 N2 O5 QSWJSOQQNWMPME-UHFFFAOYSA-N
EDO	A, B	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.249 
• R-Value Work: 0.190 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 101.810	α = 90.00
b = 149.190	β = 90.00
c = 57.240	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-11 
• Released Date: 2016-01-13 
• Deposition Author(s): Nowak, R., Velupillai, S., Krojer, T., Gileadi, C., Johansson, C., Korczynska, M., Le, D.D., Younger, N., Gregori-Puigjane, E., Tumber, A., Iwasa, E., Pollock, S.B., Ortiz Torres, I., Kopec, J., Tallant, C., Froese, S., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A., Shoichet, B.K., Fujimori, D.G., Oppermann, U.

Revision History 

• Version 1.0: 2016-01-13
  Type: Initial release
• Version 1.1: 2016-03-09
  Type: Database references
• Version 1.2: 2018-01-24
  Type: Structure summary