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show all sequences of 1.14.11.B2

Characterization of a linked Jumonji domain of the KDM5/JARID1 family of histone H3 lysine 4 demethylases

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.; J. Biol. Chem. 291, 2631-2646 (2016)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene KDM5A, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+; gene KDM5B, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+; gene KDM5C, recombinant expression ofsoluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+
Homo sapiens
Engineering
Amino acid exchange
Commentary
Organism
additional information
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5B(1-755)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain. Deletion of DELTAAP has no effect on kinetics of KDM5C; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5C(1-789)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain
Homo sapiens
Inhibitors
Inhibitors
Commentary
Organism
Structure
GSK-J1
a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain; a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5BDELTAAP; a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5CDELTAAP
Homo sapiens
JIB-04
a pan-inhibitor of the Jumonji demethylase superfamily; a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5BDELTAAP; a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5CDELTAAP
Homo sapiens
additional information
structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity; structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity; structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity, hypothetical modeling of the N-terminal half of KDM5, overview
Homo sapiens
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
Michaelis-Menten kinetics of wild-type and mutant enzymes; Michaelis-Menten kinetics of wild-type and mutant enzymes
Homo sapiens
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
required for catalysis; required for catalysis; required for catalysis
Homo sapiens
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Homo sapiens
P29375
-
-
Homo sapiens
P41229
-
-
Homo sapiens
Q9UGL1
-
-
Purification (Commentary)
Commentary
Organism
recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration; recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration; recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration. Deletion of DELTAAP has no effect on kinetics of KDM5C
Homo sapiens
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
745354
Homo sapiens
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
745354
Homo sapiens
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
additional information
no activity with monomethylated H3K4
745354
Homo sapiens
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
More
KDM5 domain structure and functional analysis, overview; KDM5 domain structure and functional analysis, overview; KDM5 domain structure and functional analysis, overview
Homo sapiens
Cloned(Commentary) (protein specific)
Commentary
Organism
gene KDM5C, recombinant expression ofsoluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+
Homo sapiens
gene KDM5B, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+
Homo sapiens
gene KDM5A, recombinant expression of soluble His-SUMO-tagged enzyme in Escherichia coli strain BL21(DE3)C+
Homo sapiens
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
additional information
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5C(1-789)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain
Homo sapiens
additional information
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. Generation of a KDM5B(1-755)DELTAAP mutant by deleting ARID and PHD1 (AP) domains by connecting residues 100 and 363. The DELTAAP constructs represent the domain arrangement of the conventional Jumonji domain followed by a C-terminal helical zinc binding domain. Deletion of DELTAAP has no effect on kinetics of KDM5C
Homo sapiens
additional information
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes
Homo sapiens
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
GSK-J1
a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5CDELTAAP
Homo sapiens
GSK-J1
a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. GSK-J1 inhibits the demethylase activity of KDM5C with 8.5fold increased potency compared with that of KDM5B at 1 mM 2-oxoglutarate. Also inhibits the enzyme mutant KDM5BDELTAAP
Homo sapiens
GSK-J1
a selective inhibitor of the KDM6/KDM5 subfamilies. Docking study and identification of critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain
Homo sapiens
JIB-04
a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5CDELTAAP
Homo sapiens
JIB-04
a pan-inhibitor of the Jumonji demethylase superfamily, that is about 8fold more potent against KDM5B than against KDM5C. Also inhibits the enzyme mutant KDM5BDELTAAP
Homo sapiens
JIB-04
a pan-inhibitor of the Jumonji demethylase superfamily
Homo sapiens
additional information
structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity
Homo sapiens
additional information
structural characterization of the linked JmjN-JmjC domain for the KDM5 family for the design of KDM5 demethylase inhibitors with improved potency and selectivity, hypothetical modeling of the N-terminal half of KDM5, overview
Homo sapiens
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
Michaelis-Menten kinetics of wild-type and mutant enzymes
Homo sapiens
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
required for catalysis
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
Homo sapiens
-
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration
Homo sapiens
recombinant His-SUMO-tagged enzyme from Escherichia coli strain BL21(DE3)C+ by nickel affinity chromatography, tag cleavage overnight by Ulp-1 protease, followed by anion exchange chromatography, gel filtration, and ultrafiltration. Deletion of DELTAAP has no effect on kinetics of KDM5C
Homo sapiens
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
histone H3 N6,N6,N6-trimethyl-L-lysine4 + 2-oxoglutarate + O2
-
745354
Homo sapiens
histone H3 N6,N6-dimethyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
-
745354
Homo sapiens
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
additional information
no activity with monomethylated H3K4
745354
Homo sapiens
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
More
KDM5 domain structure and functional analysis, overview
Homo sapiens
General Information
General Information
Commentary
Organism
evolution
the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC); the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC); the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC)
Homo sapiens
malfunction
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes; internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes
Homo sapiens
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain; minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview; minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
Homo sapiens
physiological function
role for KDM5A (JARID1A/RBP2) as oncogenic driver; role for KDM5B (JARID1B/PLU1) as oncogenic driver
Homo sapiens
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC)
Homo sapiens
malfunction
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes
Homo sapiens
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
Homo sapiens
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain
Homo sapiens
physiological function
role for KDM5B (JARID1B/PLU1) as oncogenic driver
Homo sapiens
physiological function
role for KDM5A (JARID1A/RBP2) as oncogenic driver
Homo sapiens
Other publictions for EC 1.14.11.B2
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
744494
Amano
Development and crystallograp ...
Homo sapiens
Bioorg. Med. Chem.
25
2617-2624
2017
-
-
-
1
-
-
15
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
1
-
-
-
1
-
-
-
13
-
-
-
-
-
-
1
-
-
-
15
13
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
744646
Tumber
Potent and selective KDM5 inh ...
Homo sapiens
Cell Chem. Biol.
24
371-380
2017
-
-
-
1
-
-
6
-
1
1
-
10
-
4
-
-
-
-
-
3
-
-
12
-
-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
1
-
-
9
10
-
-
4
4
-
10
-
-
-
-
-
12
-
-
12
-
-
-
-
-
-
-
-
-
-
1
4
-
-
-
744866
Yu
Chromatin remodeling demethyl ...
Mus musculus
FASEB J.
32
552-567
2017
-
-
1
-
4
-
-
-
1
1
-
2
-
2
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1
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2
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1
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4
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1
1
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2
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1
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2
-
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-
-
-
-
-
-
-
-
2
2
-
-
-
745752
Liu
LincRNAFEZF1-AS1 represses p2 ...
Homo sapiens
Mol. Cancer
16
39
2017
-
-
-
-
-
-
-
-
1
1
-
3
-
1
-
-
-
-
-
3
-
-
3
-
-
-
-
-
-
-
-
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-
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-
-
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-
-
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-
1
1
-
3
-
-
-
-
-
3
-
-
3
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
745771
Vyas
Lysine-specific demethylase-1 ...
Mus musculus
Mol. Cell. Neurosci.
82
1-11
2017
-
-
1
-
1
-
-
-
-
-
-
2
-
1
-
-
-
-
-
1
-
-
3
-
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1
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1
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2
-
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1
-
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3
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
744347
Burg
Lysine-specific demethylase 1 ...
Homo sapiens
Biochemistry
55
1652-1662
2016
-
-
-
-
-
-
3
-
-
-
-
3
-
1
-
-
-
-
-
-
-
-
6
1
1
-
-
-
1
-
-
1
3
-
1
-
-
-
1
-
-
-
1
3
3
-
-
-
-
3
-
-
-
-
-
-
-
-
6
1
1
-
-
-
1
-
-
-
-
-
-
-
-
-
744653
Zhao
H3K4me3 demethylase Kdm5a is ...
Mus musculus
Cell Rep.
15
288-299
2016
-
-
-
-
-
-
-
-
2
1
-
2
-
3
-
-
-
-
-
2
-
-
2
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-
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2
1
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2
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2
-
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2
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
744762
Mariani
The H3K4me3/2 histone demethy ...
Caenorhabditis elegans
Development
143
851-863
2016
-
-
1
-
1
-
1
-
1
-
-
1
-
2
-
-
-
-
-
4
-
-
1
-
-
-
-
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-
-
-
-
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1
-
-
1
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1
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1
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1
-
-
-
-
-
4
-
-
1
-
-
-
-
-
-
-
-
-
-
4
4
-
-
-
745354
Horton
Characterization of a linked ...
Homo sapiens
J. Biol. Chem.
291
2631-2646
2016
-
-
1
-
1
-
3
1
-
1
-
6
-
3
-
-
1
-
-
-
-
-
9
1
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
-
3
-
-
9
-
2
-
3
-
6
-
-
-
3
-
-
-
-
9
3
-
-
-
-
-
-
-
-
-
4
11
-
-
-
745525
Bavetsias
8-Substituted pyrido[3,4-d]py ...
Homo sapiens
J. Med. Chem.
59
1388-1409
2016
-
-
-
-
1
-
66
-
1
1
-
5
-
2
-
-
-
-
-
2
-
-
5
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
1
-
-
127
-
-
2
2
-
5
-
-
-
-
-
4
-
-
5
-
2
-
-
-
2
-
-
-
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