Cloned (Comment) | Organism |
---|---|
gene KMD4A, recombinant expression of N-terminally His-tagged KDM4A construct (residues 1-359) in Escherichia coli, recombinant expression of N-terminally GST-tagged enzyme in Spodoptera frugiperda Sf9 cells via baculovirus transfection method | Homo sapiens |
Crystallization (Comment) | Organism |
---|---|
purified recombinant detagged enzyme in apo form and in complex with several inhibitors, hanging drop vapor diffusion method, mixing of 0.0015 ml of 7 mg/ml protein solution with 0.0015 ml of reservoir solution containing 2-16% w/v PEG 4000 and 0.1 M BTP, pH 7.5, and equilibration against 0.8 ml, 18°C, 1 week, the crystals are then soaked by addition of 750 nL of ligand solution at 10-200 mM in DMSO directly to the crystallizatin drops, followed by 4-48 h incubation at 18°C, X-ray diffraction structure determination and analysis | Homo sapiens |
Protein Variants | Comment | Organism |
---|---|---|
H188A/E190A | site-directed mutagenesis, inactive mutant | Homo sapiens |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
(R)-2-(1-(1-benzoylpiperidin-3-yl)-1H-1,2,3-triazol-4-yl)isonicotinic acid | - |
Homo sapiens | |
1-(3-(ethylsulfonyl)phenyl)-2-(4-(pyridin-2-yl)thiazol-2-yl)ethan-1-one | - |
Homo sapiens | |
1-(3-(methylsulfonyl)phenyl)-2-(4-(pyridin-2-yl)thiazol-2-yl)ethan-1-one | - |
Homo sapiens | |
1-(4-(methylsulfonyl)phenyl)-2-(4-(pyridin-2-yl)thiazol-2-yl)ethan-1-one | - |
Homo sapiens | |
1-phenyl-2-(4-(pyridin-2-yl)thiazol-2-yl)ethan-1-one | - |
Homo sapiens | |
2-(1-hydroxyvinyl)isonicotinic acid | - |
Homo sapiens | |
2-(2-aminothiazol-4-yl)isonicotinamide | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
2-(2-aminothiazol-4-yl)isonicotinic acid | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
2-(2-benzamidothiazol-4-yl)isonicotinic acid | - |
Homo sapiens | |
2-(2-methylthiazol-4-yl)isonicotinic acid | - |
Homo sapiens | |
2-(thiazol-4-yl)isonicotinic acid | - |
Homo sapiens | |
3-((2-(pyridin-2-yl)-6-(1,2,4,5-tetrahydro-3H-benzo[d]azepin-3-yl)pyrimidin-4-yl)amino)propanoic acid | - |
Homo sapiens | |
3-(2-((2-aminoethyl)carbamoyl)pyridin-4-yl)benzoic acid | - |
Homo sapiens | |
4-((methyl((1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)methyl)amino)methyl)benzonitrile | - |
Homo sapiens | |
4-((methyl(2-(1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)ethyl)amino)methyl)benzonitrile | - |
Homo sapiens | |
4-(1-(2-(1-(4-oxo-3,4-dihydropyrido[3,4-d]pyrimidin-8-yl)-1H-pyrazol-4-yl)ethyl)piperidin-4-yl)benzonitrile | - |
Homo sapiens | |
4-(pyridin-2-yl)thiazol-2-amine | low inhibition activity | Homo sapiens | |
4-(pyridin-3-yl)thiazol-2-amine | low inhibition activity | Homo sapiens | |
8-(((furan-2-ylmethyl)amino)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-((4-(pyridin-2-yl)piperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-((4-methylpiperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-((4-phenylpiperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-((benzylamino)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-((dimethylamino)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(1-methyl-1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(2-aminothiazol-4-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-(4-(((3,4-dichlorobenzyl)(methyl)amino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-((dimethylamino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-((methyl(4-(methylsulfonyl)benzyl)amino)methyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-((4-fluorobenzyl) (methyl)amino)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-(4-(2-(4-((5-cyclopropyl-1,2,4-oxadiazol-3-yl)methyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(2,4-difluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(2-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(3,4-dichlorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(3,5-dichlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview; substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site, incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one which demonstrates equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, and cellular permeability in the Caco-2 assay | Homo sapiens | |
8-(4-(2-(4-(3,5-difluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(3-(trifluoromethyl)phenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site, incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 8-(4-(2-(4-(3-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one which demonstrates equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay | Homo sapiens | |
8-(4-(2-(4-(3-methoxybenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(4-(methylsulfonyl)phenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(4-(trifluoromethyl)benzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(4-chlorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-(4-(2-(4-(4-chlorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-(4-(2-(4-(4-fluorobenzyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(4-fluorophenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(4-methoxyphenyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(benzo[d][1,3]dioxol-5-ylmethyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(pyridin-3-ylmethyl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(pyridin-4-yl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-(thiophen-2-yl)piperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-benzylpiperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(2-(4-phenylpiperidin-1-yl)ethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(hydroxymethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(piperidin-1-ylmethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(4-(pyrrolidin-1-ylmethyl)-1H-pyrazol-1-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(piperidin-1-ylmethyl)pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
8-(thiazol-4-yl)pyrido[3,4-d]pyrimidin-4(3H)-one | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
8-chloropyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens | |
lithium 2-(((furan-2-ylmethyl)amino)methyl)isonicotinate | - |
Homo sapiens | |
lithium 2-((benzylamino)methyl)isonicotinate | enzyme-bound structure determination, crystal structure, overview | Homo sapiens | |
additional information | discovery and synthesis of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Enzyme-inhibitor binding structure modeling based on structure PDB 3PDQ, and determination from crystal structure, structure-function relationships, overview. No activity with 3-(methylsulfonyl)-N-(4-(pyridin-3-yl)thiazol-2-yl)benzamide, and 4-(methylsulfonyl)-N-(4-(pyridin-3-yl)thiazol-2-yl)benzamide, poor inhibition by 8-((4-phenylpiperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one; discovery and synthesis of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Enzyme-inhibitor binding structure modeling based on structure PDB 3PDQ, and determination from crystal structure, structure-function relationships, overview. No activity with 8-chloropyrido[3,4-d]pyrimidin-4(3H)-one, 4-(pyridin-3-yl)thiazol-2-amine, 3-(methylsulfonyl)-N-(4-(pyridin-3-yl)thiazol-2-yl)benzamide, and 4-(methylsulfonyl)-N-(4-(pyridin-3-yl)thiazol-2-yl)benzamide, poor inhibition by 4-(pyridin-2-yl)thiazol-2-amine, 8-(piperidin-1-ylmethyl)pyrido[3,4-d]pyrimidin-4(3H)-one, and 8-((4-phenylpiperazin-1-yl)methyl)pyrido[3,4-d]pyrimidin-4(3H)-one | Homo sapiens | |
pyrido[3,4-d]pyrimidin-4(3H)-one | - |
Homo sapiens |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
nucleus | - |
Homo sapiens | 5634 | - |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Fe2+ | dependent on, active site bound, required for activity | Homo sapiens |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3 N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2 | Homo sapiens | - |
histone H3 N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Homo sapiens | O75164 | - |
- |
Homo sapiens | O94953 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant N-terminally GST-tagged enzyme from Spodoptera frugiperda Sf9 cells by glutathione affinity chromatography and gel filtration, recombinant N-terminally His-tagged KDM4A 1-359 from Escherichia coli by nickel affinity chromatography, followed by tag removal with TEV protease, another step of nickel affinity chromatography using the eluate, and gel filtration | Homo sapiens |
Source Tissue | Comment | Organism | Textmining |
---|---|---|---|
Caco-2 cell | - |
Homo sapiens | - |
HeLa cell | - |
Homo sapiens | - |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
histone H3 N6,N6,N6-trimethyl-L-lysine9 + 2-oxoglutarate + O2 | - |
Homo sapiens | histone H3 N6,N6-dimethyl-L-lysine9 + succinate + formaldehyde + CO2 | - |
? | |
additional information | the enzyme is also active on histone H3 N6,N6,N6-trimethyl-L-lysine36, cf. EC 1.14.11.27 | Homo sapiens | ? | - |
? |
Synonyms | Comment | Organism |
---|---|---|
JMJD2A | - |
Homo sapiens |
JMJD2B | - |
Homo sapiens |
KDM4A | - |
Homo sapiens |
KDM4B | - |
Homo sapiens |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
22 | - |
assay at room temperature | Homo sapiens |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Homo sapiens |