ISDA

Deposition Date 2015-11-27

Release Date 2016-01-27

Last Version Date 2025-04-09

Entry Detail

PDB ID:

5FPA

Keywords:

OXIDOREDUCTASE

Title:

Crystal structure of human KDM4D in complex with 3H,4H-pyrido-3,4-d- pyrimidin-4-one

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.96 Å

R-Value Free:

0.21

R-Value Work:

0.16

R-Value Observed:

0.17

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

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
CSX	A	CYS	S-OXY CYSTEINE

Ligand Molecules

N5J

SO4

Primary Citation

Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives.

Westaway, S.M, Preston, A.G.S, Barker, M.D, Brown, F, Brown, J.A, Campbell, M, Chung, C, Diallo, H, Douault, C, Drewes, G, Eagle, R, Gordon, L, Haslam, C, Hayhow, T.G, Humphreys, P.G, Joberty, G, Katso, R, Kruidenier, L, Leveridge, M, Liddle, J, Mosley, J, Muelbaier, M, Randle, R, Rioja, I, Rueger, A, Seal, G.A, Sheppard, R.J, Singh, O, Taylor, J, Thomas, P, Thomson, D, Wilson, D.M, Lee, K, Prinjha, R.K.Show

J.Med.Chem. 59 1357 ? (2016)

PMID: 26771107 DOI: 10.1021/ACS.JMEDCHEM.5B01537

Abstact

Optimization of KDM6B (JMJD3) HTS hit 12 led to the identification of 3-((furan-2-ylmethyl)amino)pyridine-4-carboxylic acid 34 and 3-(((3-methylthiophen-2-yl)methyl)amino)pyridine-4-carboxylic acid 39 that are inhibitors of the KDM4 (JMJD2) family of histone lysine demethylases. Compounds 34 and 39 possess activity, IC50 ≤ 100 nM, in KDM4 family biochemical (RFMS) assays with ≥ 50-fold selectivity against KDM6B and activity in a mechanistic KDM4C cell imaging assay (IC50 = 6-8 μM). Compounds 34 and 39 are also potent inhibitors of KDM5C (JARID1C) (RFMS IC50 = 100-125 nM).

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Primary Citation of related structures