5A3T

Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.

Johansson, C.Velupillai, S.Tumber, A.Szykowska, A.Hookway, E.S.Nowak, R.P.Strain-Damerell, C.Gileadi, C.Philpott, M.Burgess-Brown, N.Wu, N.Kopec, J.Nuzzi, A.Steuber, H.Egner, U.Badock, V.Munro, S.Lathangue, N.B.Westaway, S.Brown, J.Athanasou, N.Prinjha, R.Brennan, P.E.Oppermann, U.

(2016) Nat.Chem.Biol. 12: 539

  • DOI: 10.1038/nchembio.2087
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal ...

    Members of the KDM5 (also known as JARID1) family are 2-oxoglutarate- and Fe(2+)-dependent oxygenases that act as histone H3K4 demethylases, thereby regulating cell proliferation and stem cell self-renewal and differentiation. Here we report crystal structures of the catalytic core of the human KDM5B enzyme in complex with three inhibitor chemotypes. These scaffolds exploit several aspects of the KDM5 active site, and their selectivity profiles reflect their hybrid features with respect to the KDM4 and KDM6 families. Whereas GSK-J1, a previously identified KDM6 inhibitor, showed about sevenfold less inhibitory activity toward KDM5B than toward KDM6 proteins, KDM5-C49 displayed 25-100-fold selectivity between KDM5B and KDM6B. The cell-permeable derivative KDM5-C70 had an antiproliferative effect in myeloma cells, leading to genome-wide elevation of H3K4me3 levels. The selective inhibitor GSK467 exploited unique binding modes, but it lacked cellular potency in the myeloma system. Taken together, these structural leads deliver multiple starting points for further rational and selective inhibitor design.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Headington, UK.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Stevenage, UK.,Department of Oncology, University of Oxford, Oxford, UK.,Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK.,Bayer Healthcare Pharmaceuticals, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSINE-SPECIFIC DEMETHYLASE 5B
A
481Homo sapiensMutation(s): 0 
Gene Names: KDM5B (JARID1B, PLU1, RBBP2H1)
EC: 1.14.11.-
Find proteins for Q9UGL1 (Homo sapiens)
Go to Gene View: KDM5B
Go to UniProtKB:  Q9UGL1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MMK
Query on MMK

Download SDF File 
Download CCD File 
A
2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid
C15 H22 N4 O3
RTKGUAPXWDCFNW-BQYQJAHWSA-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
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMKKi: 1 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.199 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 141.852α = 90.00
b = 141.852β = 90.00
c = 151.509γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4-AUTOMRphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2016-06-01
    Type: Database references
  • Version 1.3: 2016-06-29
    Type: Database references