ISDA

Deposition Date 2018-06-10

Release Date 2018-11-21

Last Version Date 2023-10-11

Entry Detail

PDB ID:

6DQ6

Keywords:

OXIDOREDUCTASE/INHIBITOR

Title:

LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.59 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.18

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Linked KDM5A Jmj Domain
Gene (Uniprot):KDM5A
Chain IDs:A
Chain Length:330
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P29375 Pfam ID:PF02375, PF02373 EC:1.14.11.67

Ligand Molecules

DMS

GOL

H6J

Primary Citation

Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.

Horton, J.R, Woodcock, C.B, Chen, Q, Liu, X, Zhang, X, Shanks, J, Rai, G, Mott, B.T, Jansen, D.J, Kales, S.C, Henderson, M.J, Cyr, M, Pohida, K, Hu, X, Shah, P, Xu, X, Jadhav, A, Maloney, D.J, Hall, M.D, Simeonov, A, Fu, H, Vertino, P.M, Cheng, X, Horton, J.R, Liu, X, Gale, M, Wu, L, Shanks, J.R, Zhang, X, Webber, P.J, Bell, J.S, Kales, S.C, Mott, B.T, Rai, G, Jansen, D.J, Henderson, M.J, Urban, D.J, Hall, M.D, Simeonov, A, Maloney, D.J, Johns, M.A, Fu, H, Jadhav, A, Vertino, P.M, Yan, Q, Cheng, X, Horton, J.R, Engstrom, A, Zoeller, E.L, Liu, X, Shanks, J.R, Zhang, X, Johns, M.A, Vertino, P.M, Fu, H, Cheng, X, Horton, J.R, Liu, X, Wu, L, Zhang, K, Shanks, J, Zhang, X, Rai, G, Mott, B.T, Jansen, D.J, Kales, S.C, Henderson, M.J, Pohida, K, Fang, Y, Hu, X, Jadhav, A, Maloney, D.J, Hall, M.D, Simeonov, A, Fu, H, Vertino, P.M, Yan, Q, Cheng, X.Show

J. Med. Chem. 61 10588 10601 (2018)

PMID: 30392349 DOI: 10.1021/acs.jmedchem.8b01219

Abstact

The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.

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Primary Citation of related structures