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BDBM191598

E3L007996

Internal ID: BDB007996

Activity data available Local docking-ready structure

Dock with P29375 Dock with P41229 Dock with Q8NHM5 Dock with Q9BY66

Structure

/e3_file/ligand_db/generated/BDB007996/BDB007996.sdf

Basic Properties

Compound ID

E3L007996

Internal ID

BDB007996

Molecular formula

C15H24N4O3

Molecular weight

308.382000

Exact mass

308.184841

XLogP

0.2795

TPSA

85.7700

HBA / HBD

5 / 2

Rotatable bonds

Heavy atoms / rings

22 / 1

Activity summary

IC50 unknown 1.40000000 nM
21 activity record(s) imported

InChIKey

RGGMVQDDHDCRDM-UHFFFAOYSA-N

SMILES

CCN(CCN(C)C)C(=O)CNCc1cc(C(=O)O)ccn1

Aliases

BDBM191598 (preferred) 2-(((2-((2-(Dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid (source_name) BDBM191598 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
P29375	KDM5A;JARID1A;RBBP2;RBP2 Lysine-specific demethylase 5A	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191598	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191598	medium ; target=Lysine-specific demethylase 5C
Q8NHM5	KDM2B;CXXC2;FBL10;FBXL10;JHDM1B;NDY1;PCCX2 Lysine-specific demethylase 2B	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191598	medium ; target=Lysine-specific demethylase 2B
Q9BY66	KDM5D;HY;HYA;JARID1D;KIAA0234;SMCY Lysine-specific demethylase 5D	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191598	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM191598	Open	-	10.1016/j.chembiol.2017.02.006; 10.7270/Q2N01BRW; 10.7270/Q25Q51RK; 10.1016/j.chembiol.2016.06.006; 10.1038/nchembio.2087; 10.1021/acs.jmedchem.5b01758 PMID: 28262558; 34555614; 38168630; 27427228; 27214403; 26710088
PubChem	CID86346639	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CCN(CCN(C)C)C(=O)CNCc1cc(C(=O)O)ccn1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007996/BDB007996.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007996/BDB007996.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007996/BDB007996.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB007996/BDB007996.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB007996/BDB007996.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM191598	IC50	100 nM	High	DOI: 10.1021/acs.jmedchem.5b01758 PMID: 26710088	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	25 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	4800 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	1.4 nM	Very high	DOI: 10.7270/Q25Q51RK PMID: 38168630	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	10 nM	Very high	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	40 nM	High	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	7 nM	Very high	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	IC50	25 nM	High	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191598	Kd	52 nM	High	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	100 nM	High	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	9.9 nM	Very high	DOI: 10.7270/Q25Q51RK PMID: 38168630	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	20 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	1000 nM	Moderate	DOI: 10.1021/acs.jmedchem.5b01758 PMID: 26710088	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	<100 nM	High	DOI: 10.1021/acs.jmedchem.5b01758 PMID: 26710088	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	59 nM	High	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	13 nM	High	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	15000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191598	IC50	59 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM191598	IC50	15 nM	High	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM191598	IC50	20 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM191598	IC50	14000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1