6DQE

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid

• PDB DOI: https://doi.org/10.2210/pdb6DQE/pdb

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


• Deposited: 2018-06-10 Released: 2019-06-12 
• Deposition Author(s): Horton, J.R., Cheng, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.187 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Literature

To be determined

Horton, J.R., Liu, X., Woodcock, C.B., Shanks, J., Zhang, X., Rai, G., Mott, B., Jansen, D.J., Kales, S., Henderson, M.J., Pohida, K., Fang, Y., Hu, X., Jadhav, A., Maloney, D., Hall, M.D., Simeonov, A., Fu, H., Vertino, P.M., Cheng, X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.81 kDa 
• Atom Count: 2,632 
• Modelled Residue Count: 294 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linked KDM5A Jmj Domain	A	330	Homo sapiens	Mutation(s): 0  Gene Names: KDM5A, JARID1A, RBBP2, RBP2 EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens) Explore P29375  Go to UniProtKB:  P29375
PHAROS:  P29375 GTEx:  ENSG00000073614

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H6A (Subject of Investigation/LOI)	B [auth A]	2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid C29 H30 N4 O3 HAJRSCRWEDXEKU-MUUNZHRXSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.187 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.924	α = 90
b = 61.803	β = 92.38
c = 46.723	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Horton, J.R., Cheng, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description