E3Docker 2.0

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Kdoam-25

E3L010306

Internal ID: BDB010306

Activity data available Local docking-ready structure

Dock with P29375 Dock with P41229 Dock with Q9BY66

Structure

/e3_file/ligand_db/generated/BDB010306/BDB010306.sdf

Basic Properties

Compound ID

E3L010306

Internal ID

BDB010306

Molecular formula

C15H25N5O2

Molecular weight

307.398000

Exact mass

307.200825

XLogP

-0.3198

TPSA

91.5600

HBA / HBD

5 / 2

Rotatable bonds

Heavy atoms / rings

22 / 1

Activity summary

IC50 unknown 27.00000000 nM
18 activity record(s) imported

InChIKey

PNFMVADNCOGWME-UHFFFAOYSA-N

SMILES

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

Aliases

BDBM223320 (preferred) Kdoam-25 (source_name) BDBM223320 (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:BDBM223320	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM223320	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:BDBM223320	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM223320	Open	-	10.1016/j.chembiol.2017.02.006; 10.1021/acs.jmedchem.8b00261; 10.1016/j.bmc.2018.03.030; 10.7270/Q2W95F76; 10.7270/Q2N01BRW PMID: 28262558; 29537847; 29764755; 35838529; 34555614
PubChem	CID91810435	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(N)=O)ccn1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010306/BDB010306.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010306/BDB010306.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010306/BDB010306.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010306/BDB010306.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010306/BDB010306.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	18000 nM	Low	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	1700 nM	Low	DOI: 10.1016/j.bmc.2018.03.030 PMID: 29764755	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	558 nM	Moderate	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	80 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	71 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	27 nM	High	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	IC50	71 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223320	Kd	2700 nM	Low	DOI: 10.1021/acs.jmedchem.8b00261 PMID: 29537847	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223320	IC50	27 nM	High	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223320	IC50	69 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223320	IC50	69 nM	High	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223320	IC50	60 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223320	IC50	558 nM	Moderate	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223320	IC50	27 nM	High	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223320	IC50	69 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223320	IC50	558 nM	Moderate	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223320	IC50	60 nM	High	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1