ISDA

Deposition Date 2012-02-08

Release Date 2012-10-03

Last Version Date 2023-12-20

Entry Detail

PDB ID:

4AI9

Keywords:

OXIDOREDUCTASE

Title:

JMJD2A Complexed with Daminozide

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.25 Å

R-Value Free:

0.23

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:LYSINE-SPECIFIC DEMETHYLASE 4A
Gene (Uniprot):KDM4A
Chain IDs:A, B
Chain Length:381
Number of Molecules:2
Biological Source:HOMO SAPIENS

UniProt ID:O75164 Pfam ID:PF02375, PF02373 EC:1.14.11.27

Ligand Molecules

DZA

GOL

Primary Citation

Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.

Rose, N.R, Woon, E.C, Tumber, A, Walport, L.J, Chowdhury, R, Li, X.S, King, O.N, Lejeune, C, Ng, S.S, Krojer, T, Chan, M.C, Rydzik, A.M, Hopkinson, R.J, Che, K.H, Daniel, M, Strain-Damerell, C, Gileadi, C, Kochan, G, Leung, I.K, Dunford, J, Yeoh, K.K, Ratcliffe, P.J, Burgess-Brown, N, von Delft, F, Muller, S, Marsden, B, Brennan, P.E, McDonough, M.A, Oppermann, U, Klose, R.J, Schofield, C.J, Kawamura, A.Show

J. Med. Chem. 55 6639 6643 (2012)

PMID: 22724510 DOI: 10.1021/jm300677j

Abstact

The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related oxygenases. Results led to the finding that daminozide (N-(dimethylamino)succinamic acid, 160 Da), a plant growth regulator, selectively inhibits the KDM2/7 JmjC subfamily. Kinetic and crystallographic studies reveal that daminozide chelates the active site metal via its hydrazide carbonyl and dimethylamino groups.

Legend

Protein

Chemical

Disease

Primary Citation of related structures