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 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/nchembio.2085
  • Primary Citation of Related Structures:  
    5CEH

  • 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 KDM5 inhibitor CPI-455 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-specific demethylase 5A790Homo sapiensMutation(s): 0 
Gene Names: KDM5A, JARID1A, RBBP2, RBP2
EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens)
Explore P29375 
Go to UniProtKB:  P29375
PHAROS:  P29375
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29375
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown Peptide10Homo sapiensMutation(s): 0 
Gene Names: KDM5A, JARID1A, RBBP2, RBP2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
50P
Query on 50P
Download Ideal Coordinates CCD File 
F [auth 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 Ideal Coordinates CCD File 
D [auth A],
E [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NI
Query on NI
Download Ideal Coordinates CCD File 
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
50P BindingDB:  5CEH IC50: min: 10, max: 506 (nM) from 3 assay(s)
EC50: 5200 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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