6H4P

Crystal structure of human KDM4A in complex with compound 16a

6H4P の概要

• エントリーDOI: 10.2210/pdb6h4p/pdb
• 分子名称: Lysine-specific demethylase 4A, ZINC ION, 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one, ... (7 entities in total)
• 機能のキーワード: histone demethylase, inhibitor, transcription, oxidoreductase
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 170589.81

構造登録者

Le Bihan, Y.V.,van Montfort, R.L.M. (登録日: 2018-07-23, 公開日: 2019-06-12, 最終更新日: 2024-01-17)

主引用文献

Le Bihan, Y.V.,Lanigan, R.M.,Atrash, B.,McLaughlin, M.G.,Velupillai, S.,Malcolm, A.G.,England, K.S.,Ruda, G.F.,Mok, N.Y.,Tumber, A.,Tomlin, K.,Saville, H.,Shehu, E.,McAndrew, C.,Carmichael, L.,Bennett, J.M.,Jeganathan, F.,Eve, P.,Donovan, A.,Hayes, A.,Wood, F.,Raynaud, F.I.,Fedorov, O.,Brennan, P.E.,Burke, R.,van Montfort, R.L.M.,Rossanese, O.W.,Blagg, J.,Bavetsias, V.
C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays.
Eur.J.Med.Chem., 177:316-337, 2019

PubMed Abstract: Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.

PubMed: 31158747
DOI: 10.1016/j.ejmech.2019.05.041

実験手法

X-RAY DIFFRACTION (2.19 Å)