6DQ8

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N49 i.e. 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.

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

(2018) J Med Chem 61: 10588-10601

  • DOI: 10.1021/acs.jmedchem.8b01219
  • Primary Citation of Related Structures:  
    6DQB, 6DQA, 6DQ4, 6DQ6, 6DQ5, 6DQ8, 6DQ9

  • PubMed Abstract: 
  • The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active ...

    The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.


    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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H6S
Query on H6S

Download CCD File 
A
2-[(R)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid
C22 H23 Cl N2 O3 S
CKHGFLIUOABPPV-VBKZILBWSA-N
 Ligand Interaction
H6T
Query on H6T

Download CCD File 
A
2-[(S)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid
C22 H23 Cl N2 O3 S
CKHGFLIUOABPPV-XOBRGWDASA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 %)
H6SKd:  260   nM  Binding MOAD
H6TKd:  260   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.253α = 90
b = 61.754β = 92.33
c = 46.718γ = 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: 2018-11-21
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence