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Additional file 1: Fig. S1. Schematic diagram of KDM4B inhibitor discovery from a library of natural products. Fig. S2. Analysis of interaction residues in the KDM4B-compound models. (A) The docked KDM4B·myricetin complex. Myricetin, M, occupied the catalytic pocket of KDM4B. (B) 2D diagram of KDM4B·myricetin interaction. Myricetin has seven H bonds, two Pi-anion, one Pi-Pi stacked, one Pi-Pi T-shaped, and one interaction with KDM4B. Fig. S3. The $$2{F}_{o}-{F}_{c}$$ 2 F o - F c map of 63S0 in the liganded complex, contoured at 1.5 σ. The bound 63S0 is drawn as heavy blue sticks. The interacting residues are drawn in thin grey sticks. The oxygen and nitrogen atoms are colored in red and blue, respectively. The Nickel ion is drawn in green. Fig. S4. Superposition of KDM4A and KDM4B structures. (A) The KDM4A⋅63S0 crystal structure (orange) and the modeled KDM4B⋅myricetin structure (slate blue) are superimposed. (B) Superposition of active-site residues based on (A). The bound 63S0 and the nearby residues are shown as thin sticks. Myricetin and the surrounding residues are shown as thick sticks. The oxygen and nitrogen atoms are red and blue, respectively. Table S1. Inhibition effect of selected compounds from TCM database on KDM4B. Table S2. Inhibition effects of analogues based on a myricetin’s fragment, (4-phenylpiperazine-1-yl) (phenyl) methanone, on KDM4A. Table S3. Inhibition effects of analogues based on a myricetin’s fragment, (E)-N'-(benzylidene) isonicotinohydrazide, on KDM4A. Table S4. Inhibition effects of analogues based on a myricetin’s fragment, pyrocatechol, on KDM4A. Table S5. Crystallographic data and refinement statistics.