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BDBM50652776

E3L065421

Internal ID: BDB065421

Activity data available Local docking-ready structure

Dock with P29375 Dock with P41229 Dock with Q8NHM5

Structure

/e3_file/ligand_db/generated/BDB065421/BDB065421.sdf

Basic Properties

Compound ID

E3L065421

Internal ID

BDB065421

Molecular formula

C24H27N5O2

Molecular weight

417.513000

Exact mass

417.216475

XLogP

3.5089

TPSA

80.2400

HBA / HBD

7 / 1

Rotatable bonds

Heavy atoms / rings

31 / 4

Activity summary

IC50 > 1.00000000 nM
3 activity record(s) imported

InChIKey

LQPGVGSKBNXQDU-UHFFFAOYSA-N

SMILES

CCOC(=O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2cccnc2)n1

Aliases

BDBM50652776 (preferred) Ethyl 3-[[2-pyridin-3-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoate (source_name) BDBM50652776 (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:BDBM50652776	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50652776	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:BDBM50652776	medium ; target=Lysine-specific demethylase 2B

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50652776	Open	-	10.7270/Q2C2525P PMID: 25279926
PubChem	CID78243729	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CCOC(=O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2cccnc2)n1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB065421/BDB065421.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB065421/BDB065421.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB065421/BDB065421.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB065421/BDB065421.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB065421/BDB065421.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM50652776	IC50	2.4 nM	Very high	DOI: 10.7270/Q2C2525P PMID: 25279926	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50652776	IC50	>5 nM	Uncertain	DOI: 10.7270/Q2C2525P PMID: 25279926	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM50652776	IC50	>1 nM	Uncertain	DOI: 10.7270/Q2C2525P PMID: 25279926	1