E3Docker 2.0

Kdoam-29

E3L010305

Internal ID: BDB010305

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB010305/BDB010305.sdf

Basic Properties

Compound ID

E3L010305

Internal ID

BDB010305

Molecular formula

C17H29N5O2

Molecular weight

335.452000

Exact mass

335.232125

XLogP

0.2831

TPSA

68.7800

HBA / HBD

5 / 1

Rotatable bonds

Heavy atoms / rings

24 / 1

Activity summary

IC50 unknown 300.00000000 nM
5 activity record(s) imported

InChIKey

VHKSSHRSJGZQOV-UHFFFAOYSA-N

SMILES

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

Aliases

BDBM223319 (preferred) Kdoam-29 (source_name) BDBM223319 (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:BDBM223319	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM223319	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:BDBM223319	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM223319	Open	-	10.1016/j.chembiol.2017.02.006; 10.7270/Q2N01BRW PMID: 28262558; 34555614
PubChem	CID126961673	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(=O)N(C)C)ccn1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010305/BDB010305.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010305/BDB010305.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010305/BDB010305.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010305/BDB010305.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010305/BDB010305.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223319	IC50	300 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223319	IC50	6500 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223319	IC50	800 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223319	IC50	6100 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223319	IC50	1000 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1