ISDA

Deposition Date 2015-11-27

Release Date 2016-11-09

Last Version Date 2024-05-08

Entry Detail

PDB ID:

5FP7

Keywords:

INHIBITOR

Title:

Crystal structure of human KDM4D in complex with 3-4-methylthiophen-2- yl methylaminopyridine-4-carboxylic acid

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 43 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LYSINE-SPECIFIC DEMETHYLASE 4D
Gene (Uniprot):KDM4D
Chain IDs:A
Chain Length:334
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:Q6B0I6 Pfam ID:PF02375, PF02373 EC:1.14.11.27

Ligand Molecules

FE2

GOL

SO4

YC8

Primary Citation

Cell Penetrant Inhibitors of the KDM4 and KDM5 Families of Histone Lysine Demethylases. 2. Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives.

Westaway, S.M, Preston, A.G, Barker, M.D, Brown, F, Brown, J.A, Campbell, M, Chung, C.W, Drewes, G, Eagle, R, Garton, N, Gordon, L, Haslam, C, Hayhow, T.G, Humphreys, P.G, Joberty, G, Katso, R, Kruidenier, L, Leveridge, M, Pemberton, M, Rioja, I, Seal, G.A, Shipley, T, Singh, O, Suckling, C.J, Taylor, J, Thomas, P, Wilson, D.M, Lee, K, Prinjha, R.K.Show

J. Med. Chem. 59 1370 1387 (2016)

PMID: 26771203 DOI: 10.1021/acs.jmedchem.5b01538

Abstact

Following the discovery of cell penetrant pyridine-4-carboxylate inhibitors of the KDM4 (JMJD2) and KDM5 (JARID1) families of histone lysine demethylases (e.g., 1), further optimization led to the identification of non-carboxylate inhibitors derived from pyrido[3,4-d]pyrimidin-4(3H)-one. A number of exemplars such as compound 41 possess interesting activity profiles in KDM4C and KDM5C biochemical and target-specific, cellular mechanistic assays.

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Primary Citation of related structures