Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 90.87 kDa 
• Atom Count: 6094 
• Modelled Residue Count: 698 
• Deposited Residue Count: 762 
• Unique protein chains: 1

5A7O

Crystal structure of human JMJD2A in complex with compound 42

• PDB DOI: 10.2210/pdb5A7O/pdb

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


• Deposited: 2015-07-09 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., Pinkas, D.M., 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: 2.15 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 

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:  
  5A7N, 5A7O, 5A7P, 5A7Q, 5A7S, 5A7W, 5A80


• 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: 

Botnar Research Center, University of Oxford , Oxford OX3 7LD, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 4A	A, B	381	Homo sapiens	Mutation(s): 0  Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7WH	D [auth A], T [auth B]	2-[5-(2-methoxyethanoylamino)-2-oxidanyl-phenyl]pyridine-4-carboxylic acid C15 H14 N2 O5 HHHINYOXTBYXCI-UHFFFAOYSA-N
SO4	C [auth A], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	BA [auth B], R [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	P [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	AA [auth B], Q [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.91	α = 90
b = 149.13	β = 90
c = 57.09	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-09 
• 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., Pinkas, D.M., 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
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Advisory, Structure summary