E3Docker 2.0

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Kdm5-C70

E3L007997

Internal ID: BDB007997

Activity data available Local docking-ready structure

Dock with P29375 Dock with P41229 Dock with Q9BY66

Structure

/e3_file/ligand_db/generated/BDB007997/BDB007997.sdf

Basic Properties

Compound ID

E3L007997

Internal ID

BDB007997

Molecular formula

C17H28N4O3

Molecular weight

336.436000

Exact mass

336.216141

XLogP

0.7580

TPSA

74.7700

HBA / HBD

6 / 1

Rotatable bonds

Heavy atoms / rings

24 / 1

Activity summary

IC50 unknown 60.00000000 nM
12 activity record(s) imported

InChIKey

WCILOMUUNVPIKQ-UHFFFAOYSA-N

SMILES

CCOC(=O)c1ccnc(CNCC(=O)N(CC)CCN(C)C)c1

Aliases

BDBM191599 (preferred) Kdm5-C70 (source_name) BDBM191599 (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:BDBM191599	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191599	medium ; target=Lysine-specific demethylase 5C
Q9BY66	KDM5D;HY;HYA;JARID1D;KIAA0234;SMCY Lysine-specific demethylase 5D	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM191599	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM191599	Open	-	10.1016/j.chembiol.2017.02.006; 10.7270/Q2N01BRW; 10.1016/j.chembiol.2016.06.006; 10.1021/acs.jmedchem.5b01758 PMID: 28262558; 34555614; 27427228; 26710088
PubChem	CID90094283	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CCOC(=O)c1ccnc(CNCC(=O)N(CC)CCN(C)C)c1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007997/BDB007997.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007997/BDB007997.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB007997/BDB007997.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB007997/BDB007997.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB007997/BDB007997.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191599	IC50	303 nM	Moderate	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191599	IC50	60 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191599	IC50	303 nM	Moderate	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191599	IC50	103000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM191599	Kd	>10000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191599	IC50	<1000 nM	Uncertain	DOI: 10.1021/acs.jmedchem.5b01758 PMID: 26710088	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191599	IC50	580 nM	Moderate	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191599	IC50	580 nM	Moderate	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191599	IC50	330000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM191599	IC50	200 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM191599	IC50	100 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM191599	IC50	290000 nM	Low	DOI: 10.1016/j.chembiol.2016.06.006 PMID: 27427228	1