E3Docker 2.0

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Kdm5A-IN-1

E3L012775

Internal ID: BDB012775

Activity data available Local docking-ready structure

Dock with P29375 Dock with P41229 Dock with Q8NHM5

Structure

/e3_file/ligand_db/generated/BDB012775/BDB012775.sdf

Basic Properties

Compound ID

E3L012775

Internal ID

BDB012775

Molecular formula

C15H22N4O2

Molecular weight

290.367000

Exact mass

290.174276

XLogP

1.2738

TPSA

78.0900

HBA / HBD

3 / 2

Rotatable bonds

Heavy atoms / rings

21 / 3

Activity summary

IC50 unknown 0.04900000 nM
12 activity record(s) imported

InChIKey

CXEXTVGTDZRKJS-LLVKDONJSA-N

SMILES

CC(C)c1cc(C(=O)N2CC[C@@H](NC(=O)C3CC3)C2)[nH]n1

Aliases

BDBM281089 (preferred) Kdm5A-IN-1 (source_name) BDBM281089 (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:BDBM281089	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM281089	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:BDBM281089	medium ; target=Lysine-specific demethylase 2B

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM281089	Open	-	10.7270/Q2PC34F7; 10.1021/acs.jmedchem.8b00261; 10.1016/j.bmcl.2017.05.016; 10.7270/Q2N01BRW PMID: 29537847; 28512031; 34555614
PubChem	CID119081409	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CC(C)c1cc(C(=O)N2CC[C@@H](NC(=O)C3CC3)C2)[nH]n1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB012775/BDB012775.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB012775/BDB012775.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB012775/BDB012775.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB012775/BDB012775.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB012775/BDB012775.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM281089	IC50	>25000 nM	Low	DOI: 10.1016/j.bmcl.2017.05.016 PMID: 28512031	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	45 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	22000 nM	Low	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	570 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	45 nM	High	DOI: 10.1016/j.bmcl.2017.05.016 PMID: 28512031	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	2400 nM	Low	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	<500 nM	Uncertain	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	IC50	0.049 nM	Very high	DOI: 10.7270/Q2PC34F7	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	EC50	960 nM	Moderate	DOI: 10.1016/j.bmcl.2017.05.016 PMID: 28512031	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM281089	Kd	2400 nM	Low	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM281089	IC50	55 nM	High	DOI: 10.1016/j.bmcl.2017.05.016 PMID: 28512031	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM281089	IC50	65 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1