5CEH

Structure of histone lysine demethylase KDM5A in complex with selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells.

Vinogradova, M.Gehling, V.S.Gustafson, A.Arora, S.Tindell, C.A.Wilson, C.Williamson, K.E.Guler, G.D.Gangurde, P.Manieri, W.Busby, J.Flynn, E.M.Lan, F.Kim, H.J.Odate, S.Cochran, A.G.Liu, Y.Wongchenko, M.Yang, Y.Cheung, T.K.Maile, T.M.Lau, T.Costa, M.Hegde, G.V.Jackson, E.Pitti, R.Arnott, D.Bailey, C.Bellon, S.Cummings, R.T.Albrecht, B.K.Harmange, J.C.Kiefer, J.R.Trojer, P.Classon, M.

(2016) Nat Chem Biol 12: 531-538

  • DOI: 10.1038/nchembio.2085
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KD ...

    The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KDM5 inhibitor CPI-455. The crystal structure of KDM5A revealed the mechanism of inhibition of CPI-455 as well as the topological arrangements of protein domains that influence substrate binding. CPI-455 mediated KDM5 inhibition, elevated global levels of H3K4 trimethylation (H3K4me3) and decreased the number of DTPs in multiple cancer cell line models treated with standard chemotherapy or targeted agents. These findings show that pretreatment of cancer cells with a KDM5-specific inhibitor results in the ablation of a subpopulation of cancer cells that can serve as the founders for therapeutic relapse.


    Organizational Affiliation

    Genentech Inc., South San Francisco, California, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase 5A
A
790Homo sapiensMutation(s): 0 
Gene Names: KDM5AJARID1ARBBP2RBP2
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for P29375 (Homo sapiens)
Go to UniProtKB:  P29375
NIH Common Fund Data Resources
PHAROS  P29375
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Unknown Peptide
B
10Homo sapiensMutation(s): 0 
Gene Names: KDM5AJARID1ARBBP2RBP2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
50P
Query on 50P

Download CCD File 
A
7-oxo-5-phenyl-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
C16 H14 N4 O
DHXKRMSKXLDZGY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
50PIC50:  10   nM  BindingDB
50PIC50:  20   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.306α = 90
b = 159.306β = 90
c = 92.462γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-07-06
    Changes: Database references
  • Version 1.3: 2016-07-20
    Changes: Data collection
  • Version 1.4: 2017-11-22
    Changes: Derived calculations, Refinement description