6BGX

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)((4,4-difluorocyclohexyl)methoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N42)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.882 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DQB, 6DQA, 6DQ9, 6DQ8, 6DQ6, 6DQ5, 6DQ4

  • 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: 
    • 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
    • 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


    Organizational Affiliation

    Department of Molecular and Cellular Oncology , The University of Texas MD Anderson Cancer Center , Houston , Texas 77030 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A, linked KDM5A JMJ domain
A
330Homo sapiensMutation(s): 0 
Gene Names: KDM5A (JARID1A, RBBP2, RBP2)
EC: 1.14.11.-
Find proteins for P29375 (Homo sapiens)
Go to Gene View: KDM5A
Go to UniProtKB:  P29375
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DKV
Query on DKV

Download SDF File 
Download CCD File 
A
2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
C22 H21 Cl F2 N2 O3
OZTBUBVWGCXOMR-FQEVSTJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.882 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.365α = 90.00
b = 61.850β = 92.36
c = 46.541γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM049245-23

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references