ISDA

Deposition Date 2015-07-06

Release Date 2016-05-18

Last Version Date 2024-10-16

Entry Detail

PDB ID:

5CEH

Keywords:

Oxidoreductase/Inhibitor

Title:

Structure of histone lysine demethylase KDM5A in complex with selective inhibitor

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.14 Å

R-Value Free:

0.23

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 31 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Lysine-specific demethylase 5A
Gene (Uniprot):KDM5A
Chain IDs:A
Chain Length:790
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29375 Pfam ID:PF02375, PF01388, PF00628, PF02373, PF21323, PF02928 EC:1.14.11.67

Polymer Type:polypeptide(L)
Molecule:Unknown Peptide
Chain IDs:B
Chain Length:10
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

50P

Primary Citation

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.Show

Nat.Chem.Biol. 12 531 538 (2016)

PMID: 27214401 DOI: 10.1038/nchembio.2085

Abstact

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.

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Primary Citation of related structures