ISDA

Deposition Date 2016-05-20

Release Date 2016-08-10

Last Version Date 2024-10-23

Entry Detail

PDB ID:

5K4L

Keywords:

Oxidoreductase/Inhibitor

Title:

Crystal structure of KDM5A in complex with a naphthyridone inhibitor

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.18 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 31

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Lysine-specific demethylase 5A
Gene (Uniprot):KDM5A
Chain IDs:A, B
Chain Length:790
Number of Molecules:2
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:C (auth: F), D (auth: G)
Chain Length:10
Number of Molecules:2
Biological Source:Homo sapiens

Ligand Molecules

6QN

Primary Citation

Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors.

Labadie, S.S, Dragovich, P.S, Cummings, R.T, Deshmukh, G, Gustafson, A, Han, N, Harmange, J.C, Kiefer, J.R, Li, Y, Liang, J, Liederer, B.M, Liu, Y, Manieri, W, Mao, W, Murray, L, Ortwine, D.F, Trojer, P, VanderPorten, E, Vinogradova, M, Wen, L.Show

Bioorg.Med.Chem.Lett. 26 4492 4496 (2016)

PMID: 27499454 DOI: 10.1016/j.bmcl.2016.07.070

Abstact

Features from a high throughput screening (HTS) hit and a previously reported scaffold were combined to generate 1,7-naphthyridones as novel KDM5 enzyme inhibitors with nanomolar potencies. These molecules exhibited high selectivity over the related KDM4C and KDM2B isoforms. An X-ray co-crystal structure of a representative molecule bound to KDM5A showed that these inhibitors are competitive with the co-substrate (2-oxoglutarate or 2-OG).

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Primary Citation of related structures