E3Docker 2.0

< Back to small molecule database

BDBM195608

E3L008098

Internal ID: BDB008098

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/BDB008098/BDB008098.sdf

Basic Properties

Compound ID

E3L008098

Internal ID

BDB008098

Molecular formula

C16H14N4O

Molecular weight

278.315000

Exact mass

278.116761

XLogP

2.6847

TPSA

73.9500

HBA / HBD

3 / 1

Rotatable bonds

Heavy atoms / rings

21 / 3

Activity summary

IC50 unknown 10.00000000 nM
22 activity record(s) imported

InChIKey

DHXKRMSKXLDZGY-UHFFFAOYSA-N

SMILES

CC(C)c1c(-c2ccccc2)[nH]c2c(C#N)cnn2c1=O

Aliases

BDBM195608 (preferred) BDBM195608 (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:BDBM195608	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM195608	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:BDBM195608	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:BDBM195608	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM195608	Open	-	10.1038/nchembio.2085; 10.7270/Q2PV6QPC; 10.1016/j.bmc.2019.02.006; 10.1016/j.bmcl.2016.07.026; 10.7270/Q2HQ444G; 10.7270/Q2N01BRW PMID: 27214401; 30745098; 27476424; 34591474; 34555614

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CC(C)c1c(-c2ccccc2)[nH]c2c(C#N)cnn2c1=O	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008098/BDB008098.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008098/BDB008098.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008098/BDB008098.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB008098/BDB008098.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB008098/BDB008098.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM195608	IC50	9100 nM	Low	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM195608	IC50	>25000 nM	Low	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM195608	IC50	>9100 nM	Low	DOI: 10.1016/j.bmcl.2016.07.026 PMID: 27476424	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	506 nM	Moderate	DOI: 10.1016/j.bmc.2019.02.006 PMID: 30745098	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	506 nM	Moderate	DOI: 10.7270/Q2PV6QPC	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	10 nM	Very high	DOI: 10.7270/Q2HQ444G PMID: 34591474	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	10 nM	Very high	DOI: 10.1016/j.bmcl.2016.07.026 PMID: 27476424	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	20 nM	High	DOI: 10.1016/j.bmcl.2016.07.026 PMID: 27476424	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	20 nM	High	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	10 nM	Very high	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	IC50	10 nM	Very high	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195608	EC50	5200 nM	Low	DOI: 10.1016/j.bmcl.2016.07.026 PMID: 27476424	2 source records
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195608	IC50	14 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195608	IC50	14 nM	High	DOI: 10.1016/j.bmcl.2016.07.026 PMID: 27476424	2 source records
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195608	IC50	3010 nM	Low	DOI: 10.1016/j.bmc.2019.02.006 PMID: 30745098	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195608	IC50	14 nM	High	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM195608	IC50	2000 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1