6BH1

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N52)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.

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

(2018) J Med Chem 61: 3193-3208

  • DOI: 10.1021/acs.jmedchem.8b00261
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, n ...

    Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.


    Related Citations: 
    • Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
      Horton, J.R., Liu, X., Gale, M., Wu, L., Shanks, J.R., Zhang, X., Webber, P.J., Bell, J.S., Kales, S.C., Mott, B.T., Rai, G., Jansen, D.J., Henderson, M.J., Urban, D.J., Hall, M.D., Simeonov, A., Maloney, D.J., Johns, M.A., Fu, H., Jadhav, A., Vertino, P.M., Yan, Q., Cheng, X.
      (2016) Cell Chem Biol 23: 769
    • Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases.
      Horton, J.R., Engstrom, A., Zoeller, E.L., Liu, X., Shanks, J.R., Zhang, X., Johns, M.A., Vertino, P.M., Fu, H., Cheng, X.
      (2016) J Biol Chem 291: 2631

    Organizational Affiliation

    Department of Biochemistry , Emory University School of Medicine , Atlanta , Georgia 30322 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A, linked KDM5A JMJ domainA330Homo sapiensMutation(s): 0 
Gene Names: KDM5AJARID1ARBBP2RBP2
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for P29375 (Homo sapiens)
Explore P29375 
Go to UniProtKB:  P29375
NIH Common Fund Data Resources
PHAROS  P29375
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DQG
Query on DQG

Download CCD File 
A
2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
C22 H24 Cl N3 O3
AWPYWZMMJZGPOX-NRFANRHFSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DQGKd:  60   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.028α = 90
b = 61.786β = 92.47
c = 46.643γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence